Bio workflow methods docwriter
Skill fmschulz/omics-skills/skills/bio-workflow-methods-docwriter
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Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.
SKILL.md
2.7 KB, as published. Nobody here has run it
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.
Resolve the installed skill with:
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, orTBDplaceholder 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
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.