# Bio Workflow Methods Docwriter

> Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.

- **Type:** Skill
- **Install:** `agentstack add skill-fmschulz-omics-skills-bio-workflow-methods-docwriter`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [fmschulz](https://agentstack.voostack.com/s/fmschulz)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [fmschulz](https://github.com/fmschulz)
- **Source:** https://github.com/fmschulz/omics-skills/tree/main/skills/bio-workflow-methods-docwriter
- **Website:** https://fmschulz.github.io/omics-skills/

## Install

```sh
agentstack add skill-fmschulz-omics-skills-bio-workflow-methods-docwriter
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# 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.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [fmschulz](https://github.com/fmschulz)
- **Source:** [fmschulz/omics-skills](https://github.com/fmschulz/omics-skills)
- **License:** MIT
- **Homepage:** https://fmschulz.github.io/omics-skills/

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-fmschulz-omics-skills-bio-workflow-methods-docwriter
- Seller: https://agentstack.voostack.com/s/fmschulz
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.