How does this skill detect errors in my workflow?

It scans your workflow generator scripts, wrapper files, and Dockerfiles against a comprehensive checklist of known Pegasus best practices, checking for common pitfalls like path mismatches and dependency errors.

What is a Pegasus workflow?

Pegasus is a Workflow Management System used to execute large-scale scientific computations on distributed resources like clusters, grids, and clouds by mapping abstract workflows to physical resources.

Can it fix the errors automatically?

The skill provides a structured report with specific 'Fix' instructions. You can then ask Claude to apply those suggested changes directly to your Python or shell scripts.

Does it support containerized workflows?

Yes, it specifically checks Category 7 (Dockerfiles) and Category 1 (Transformation Catalog) to ensure container images and stageable scripts are configured correctly.

Why use /pegasus-review instead of standard debugging?

It automates the mental checklist of a Pegasus expert, catching subtle issues like File instance reuse and stage-out flags that often cause silent failures in distributed environments.

Pegasus Workflow Reviewer

Name: Pegasus Workflow Reviewer
Author: pegasus-isi

bypegasus-isi

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Despliegue y DevOps

Audits Pegasus scientific workflows to identify configuration errors, optimize resource usage, and ensure best practices for distributed execution.

The Pegasus Workflow Reviewer is a specialized skill designed to automate the validation and optimization of Pegasus scientific workflows. By analyzing workflow generators, wrapper scripts, and container configurations, it detects critical runtime errors such as missing dependencies, incorrect file cataloging, and inefficient resource allocations. Whether you are building complex genomic pipelines or seismic modeling simulations, this skill provides a structured audit report with actionable fixes to ensure your jobs run reliably across distributed computing environments like HTCondor, SLURM, or cloud infrastructures.

Características Principales

01Optimization of resource profiles including CPU and memory allocations for distributed jobs

02Automated validation of Transformation and Replica Catalogs for path and script integrity

03Verification of wrapper script I/O, exit code propagation, and environment setup

040 GitHub stars

05Deep analysis of Directed Acyclic Graph (DAG) dependencies and file instance consistency

06Comprehensive review of Dockerfile configurations and containerized tool integration

Casos de Uso

01Debugging failed Pegasus workflows before submitting to production clusters or grids

02Ensuring reproducibility and best practices in scientific computing research projects

03Migrating local bioinformatics pipelines to distributed cloud or HPC infrastructure

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add pegasus-isi/claude-plugin-marketplace pegasus-review

For use in Claude.ai and ChatGPT

Download Skill