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. Resolve the installed skill with: ```bash METHODS_SKILL="${METHODS_SKILL:-$HOME/.agents/skills/bio-workflow-methods-docwriter}" ``` ## Quick Reference | Task | Action | |------|--------| | Evidence checklist | See `reference/evidence-checklist.md` | | Standards to align with | See [reference/standards.md](reference/standards.md) | | Manifest schema | `schemas/run-manifest.schema.json` (LinkML source: [schemas/workflow-run-schema.yaml](schemas/workflow-run-schema.yaml)) | | Drafting templates | [METHODS.md template](templates/methods_report.md), [paper-summary YAML](templates/paper_summary.yaml) | | Extract a Nextflow draft | `uv run "$METHODS_SKILL/scripts/extract_nextflow_run.py" --help` | | Extract Snakemake evidence | `uv run --script "$METHODS_SKILL/scripts/extract_snakemake_run.py" --help` | | Extract CWL evidence | `uv run --script "$METHODS_SKILL/scripts/extract_cwl_run.py" --help` | | Validate manifest | `uv run "$METHODS_SKILL/scripts/validate_run_manifest.py" run_manifest.yaml` | | Examples | See `examples/` | ## Input Requirements -