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pegasus-review

Review Pegasus workflows for errors and best practices across multiple categories.

Updated Feb 11, 2026
Search Tags:#automation#workflow#best practices#debugging#review#pegasus
One-click install
npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-review
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pegasus-review
Source: https://github.com/pegasus-isi/pegasus-workflow-toolkit/tree/main/.claude/skills/pegasus-review
Command: npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-review

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) and scripts (resource) components.

What problem does it solve?

This Skill automates the review of Pegasus workflows, identifying common pitfalls, errors, and areas for improvement to ensure robust and efficient execution.

Core Features & Use Cases

  • Comprehensive Checklist: Evaluates workflows against categories like Transformation Catalog, Replica Catalog, DAG Correctness, File I/O, Wrapper Scripts, Resource Configuration, Dockerfile, and CLI usability.
  • Error Detection: Pinpoints critical errors that will cause runtime failures.
  • Best Practice Guidance: Offers warnings and suggestions for non-standard patterns and potential optimizations.
  • Use Case: Before submitting a complex bioinformatics workflow to Pegasus, use this Skill to automatically check for common configuration errors, ensuring it runs smoothly and avoids costly debugging cycles.

Quick Start

Use the pegasus-review skill to review the workflow in the current directory.

Frequently Asked Questions about pegasus-review

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

FAQPage Schema
How do I check my Pegasus workflow for common configuration errors before submission?▼

To review a Pegasus workflow for common configuration errors, analyze workflow generator scripts, wrapper scripts, Dockerfiles, and configuration files against Pegasus WMS standards. This automated review identifies critical runtime failures and best practice violations.

What types of files do I need to prepare for a Pegasus workflow review?▼

A Pegasus workflow review analyzes workflow generator scripts, wrapper scripts, Dockerfiles, and configuration files. Providing these files allows the review to evaluate Transformation Catalog, Replica Catalog, DAG correctness, and resource configuration.

What is the best way to validate Dockerfile and wrapper script compatibility in Pegasus WMS?▼

The best way to validate Dockerfile and wrapper script compatibility in Pegasus WMS is to perform an automated workflow review. This process checks for non-standard patterns, potential optimizations, and adherence to execution standards.

Does automated Pegasus workflow review check DAG correctness and File I/O configurations?▼

Yes, automated Pegasus workflow review checks DAG correctness and File I/O configurations. It evaluates workflows against a comprehensive checklist to pinpoint critical errors and offer best practice guidance for reliable execution.

Why does my bioinformatics workflow fail when submitted to Pegasus WMS?▼

A bioinformatics workflow might fail when submitted to Pegasus WMS due to critical errors in Transformation Catalog, Replica Catalog, or wrapper scripts. Reviewing the workflow configuration beforehand identifies these runtime failures and non-standard patterns.

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