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Bio Workflow Methods Docwriter

skill-fmschulz-omics-skills-bio-workflow-methods-docwriter · by fmschulz

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

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Install

$ agentstack add skill-fmschulz-omics-skills-bio-workflow-methods-docwriter

✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

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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

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.

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

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Versions

  • v0.1.0 Imported from the upstream source.

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