bio-workflow-methods-docwriter

name	bio-workflow-methods-docwriter
description	Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.

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.

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, or TBD placeholder 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.