Bio Workflow Methods Docwriter
Create publication-ready Methods and run documentation from real workflow artifacts.
Instructions
- Collect the workflow evidence package (logs, configs, version files).
- Build
run_manifest.yamlstrictly from evidence. - Validate the manifest against the schema.
- Draft
METHODS.mdwith a concise workflow summary at the top. - Verify QC gates and reproducibility details are captured.
Quick Reference
| Task | Action |
|---|---|
| Evidence checklist | See reference/evidence-checklist.md |
| Manifest schema | schemas/run-manifest.schema.json |
| Validate manifest | python scripts/validate_run_manifest.py run_manifest.yaml |
| Examples | See examples/ |
Input Requirements
- Workflow artifacts (Nextflow/Snakemake/CWL logs and configs)
- Tool version records or container digests
- QC reports and output manifests
Output
METHODS.md(workflow summary + detailed steps)run_manifest.yaml(machine-readable run manifest)
Quality Gates
- No invented commands, versions, or parameters
- Every step has inputs, outputs, and versions captured
- Workflow summary appears at top of
METHODS.md
Examples
Example 1: Validate a manifest
python scripts/validate_run_manifest.py run_manifest.yaml
Troubleshooting
Issue: Missing tool versions in logs
Solution: Mark as NOT CAPTURED and add a note on how to capture next time.