bio-workflow-methods-docwriter
Scannednpx machina-cli add skill fmschulz/omics-skills/bio-workflow-methods-docwriter --openclawBio 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.yaml
Troubleshooting
Issue: Missing tool versions in logs
Solution: Mark as NOT CAPTURED and add a note on how to capture next time.
Source
git clone https://github.com/fmschulz/omics-skills/blob/main/skills/bio-workflow-methods-docwriter/SKILL.mdView on GitHub Overview
Bio Workflow Methods Docwriter converts real workflow run artifacts (Nextflow, Snakemake, CWL) into publication-ready METHODS.md and a machine-readable run_manifest.yaml. It captures exact commands, versions or container digests, parameters, QC gates, inputs/outputs, and reproducibility notes to support transparent reporting.
How This Skill Works
First, collect an evidence package containing logs, configs, and version files. Then build run_manifest.yaml strictly from evidence and validate it against the schema. Finally, draft METHODS.md with a concise workflow summary and ensure QC gates and reproducibility details are captured.
When to Use It
- When you have workflow artifacts (logs/configs) and need publication-ready methods.
- When producing a machine-readable manifest for compliance or reproducibility checks.
- When you must verify QC gates and exact command/version capture before publishing.
- When preparing a manuscript's Methods section with a workflow summary at the top.
- When troubleshooting missing tool versions by marking as NOT CAPTURED and documenting the capture process.
Quick Start
- Step 1: Collect evidence package (logs, configs, versions).
- Step 2: Build run_manifest.yaml from evidence and validate it.
- Step 3: Draft METHODS.md with a concise workflow summary and verify QC gates.
Best Practices
- Collect a complete evidence package: logs, configs, version files.
- Build run_manifest.yaml strictly from evidence; avoid invented data.
- Capture exact commands, tool versions or container digests, inputs, and outputs.
- Validate the manifest against the run-manifest schema.
- Draft METHODS.md with a concise top summary and traceable reproducibility notes.
Example Use Cases
- Use the manifest validator: python scripts/validate_run_manifest.py run_manifest.yaml.
- Draft METHODS.md with a top workflow summary and step-by-step reproducible commands.
- Mark missing tool versions as NOT CAPTURED and document capture steps for next time.
- Reference evidence checklist and manifest schema during preparation.
- Inspect QC gates and outputs in the run manifest to ensure reproducibility.
