git:20260711.5ae6f6f to git:20260712.3675171

3 added, 0 removed. Audit A to A.

---

name: bio-workflow-methods-docwriter

description: Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.

---

# 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` |

| Manifest schema | `schemas/run-manifest.schema.json` |

| 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

- 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

- [ ] Commands were sourced from task scripts, not environment-bearing wrappers, and contain no credentials

- [ ] No `NOT CAPTURED`, `UNKNOWN`, or `TBD` placeholder remains in a required field

- [ ] Workflow summary appears at top of `METHODS.md`

+ - [ ] The engine-specific extractor output passes `validate_run_manifest.py`; the fixture-backed Nextflow path proves trace, task script, input, output, version, and final-output evidence end to end.

## Examples

### Example 1: Validate a manifest

```bash

METHODS_SKILL="${METHODS_SKILL:-$HOME/.agents/skills/bio-workflow-methods-docwriter}"

uv run "$METHODS_SKILL/scripts/validate_run_manifest.py" run_manifest.yaml

```

## Troubleshooting

**Issue**: Missing tool versions in logs

**Solution**: Use `NOT CAPTURED` only while assembling a draft. The final validator rejects it; recover the version from provenance or report the missing evidence in `limitations` without claiming a reproducible manifest.