bio-workflow-methods-docwriter

name	bio-workflow-methods-docwriter
description	Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs. Use when this capability is needed.
metadata	{"author":"fmschulz"}

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.

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