bio-workflow-methods-docwriterlisted

# Bio Workflow Methods Docwriter Create publication-ready Methods and run documentation from real workflow artifacts. ## Instructions 1. Collect the workflow evidence package (logs, configs, version files). 2. Build `run_manifest.yaml` strictly from evidence. 3. Validate the manifest against the schema. 4. Draft `METHODS.md` with a concise workflow summary at the top. 5. 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 ```bash 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.