canonical-preflight

Verify required project files and baseline outputs before replication runs.

Updated Apr 18, 2026
One-click install
npx skills add https://github.com/Centaurioun/osteogenesis_imperfecta --skill canonical-preflight
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: canonical-preflight
Source: https://github.com/Centaurioun/osteogenesis_imperfecta/tree/main/.claude/skills/canonical-preflight
Command: npx skills add https://github.com/Centaurioun/osteogenesis_imperfecta --skill canonical-preflight

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about canonical-preflight

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I validate required files before running a data analysis pipeline?

To validate required files before running a data analysis pipeline, run a preflight check that confirms path existence and readability of raw CSVs, codebooks, and reference documents, returning a structured JSON pass/fail report to block execution if assets are missing.

What is preflight validation for reproducible analyses?

Preflight validation for reproducible analyses is a fail-fast process that verifies required canonical inputs, baseline outputs, and reference documents exist and are accessible before launching replication runs, preventing wasted execution time and undetected failures.

How do I check if baseline output tables exist before starting a replication run?

To check if baseline output tables exist before starting a replication run, perform a baseline verification step that confirms canonical output folders and specific publication tables are present so downstream analyses can safely assume a validated baseline.

Can I generate timestamped run folders automatically when validating workspace inputs?

Yes, you can generate timestamped run folders automatically when validating workspace inputs. The preflight process creates timestamped run folders for new outputs during validation to preserve reproducibility and operational safety.

What happens if required datasets or reference documents are missing during preflight?

If required datasets or reference documents are missing during preflight, the fail-fast validation rules block execution and report the missing assets in a structured JSON pass/fail report, alerting collaborators before the pipeline launches.

Does preflight validation work for manuscript-ready data workflows?

Yes, preflight validation works for manuscript-ready data workflows by verifying canonical inputs, reference documents, and baseline outputs are present and accessible, ensuring publication tables and downstream analyses meet reproducibility standards prior to execution.