Bio Stats ML Reporting
Aggregate results, train ML models, and produce reports with validated references.
Instructions
- Join outputs in DuckDB and build feature tables.
- Train baseline models and evaluate with cross-validation.
- Generate reports and validate references.
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.mdfor expected tools. - Results tables and metadata are available. Inputs:
- results/*.parquet or results/*.tsv
- metadata.tsv
Output
- results/bio-stats-ml-reporting/models/
- results/bio-stats-ml-reporting/metrics.tsv
- results/bio-stats-ml-reporting/report.md
- results/bio-stats-ml-reporting/logs/
Quality Gates
- Model performance sanity checks pass.
- Reference validation passes.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
- Verify input tables are readable and schema-consistent.
Examples
Example 1: Expected input layout
results/*.parquet or results/*.tsv
metadata.tsvTroubleshooting
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.