bio-workflow-methods-docwriter
Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.
Resources
6Install
npx skillscat add fmschulz/omics-skills/bio-workflow-methods-docwriter Install via the SkillsCat registry.
We need to produce a 2-3 sentence plain-text summary, objective, factual, no marketing, no superlatives, no calls to action. No bullet points, no headings, no markdown. At most 60 words. Must be plain text, not wrapped in quotes. We need to explain what skill does, what problem it solves, when to use. Let's craft: "This skill extracts workflow run artifacts from Nextflow, Snakemake, or CWL executions to produce a reproducible Methods section and a machine‑readable run manifest.
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.yamlTroubleshooting
Issue: Missing tool versions in logs
Solution: Mark as NOT CAPTURED and add a note on how to capture next time.
Categories
Install
npx skillscat add fmschulz/omics-skills/bio-workflow-methods-docwriter Install via the SkillsCat registry.