canonical-preflight

What problem does it solve?

Prevents wasted runs and undetected failures by verifying that all required canonical inputs, baseline outputs, and reference documents are present and accessible before any replication or analysis execution.

Core Features & Use Cases

• Input validation: Confirms the presence and readability of required raw and reference files such as raw CSVs, codebooks, and gene maps.
• Baseline verification: Ensures canonical output folders and specific publication tables exist so downstream analyses can assume a validated baseline.
• Operational safety: Applies fail-fast rules, reports missing assets, and creates timestamped run folders for new outputs to preserve reproducibility.
• Use case: Run this skill automatically at the start of a replication pipeline to block execution and alert collaborators when required datasets or publication tables are missing.

Quick Start

Run a preflight across the workspace to confirm required inputs, baseline outputs, and reference documents are present and produce a JSON pass/fail report.