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pegasus-scaffold

Generates a complete Pegasus workflow project structure from a pipeline description.

Updated Feb 11, 2026
Search Tags:#workflow#code generation#scaffolding#data pipeline#bioinformatics#pegasus
One-click install
npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-scaffold
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pegasus-scaffold
Source: https://github.com/pegasus-isi/pegasus-workflow-toolkit/tree/main/.claude/skills/pegasus-scaffold
Command: npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-scaffold

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the creation of new Pegasus workflow projects, significantly reducing the boilerplate code and setup time required for new bioinformatics or data analysis pipelines.

Core Features & Use Cases

  • Project Scaffolding: Generates all necessary files for a new Pegasus workflow, including the workflow generator, wrapper scripts, Dockerfile, README, and manual run script.
  • Guided Configuration: Prompts the user for essential pipeline details like name, steps, data sources, parallelism patterns, and tool requirements to tailor the generated project.
  • Use Case: A researcher needs to set up a new variant calling pipeline. They can use /pegasus-scaffold to quickly generate a well-structured project template, which they can then customize with their specific tools and parameters.

Quick Start

Use the pegasus-scaffold skill to create a new workflow project named 'my-variant-calling-pipeline'.

Frequently Asked Questions about pegasus-scaffold

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

FAQPage Schema
How do I scaffold a Pegasus workflow project for a new bioinformatics pipeline?▼

Scaffolding a Pegasus workflow project automates the creation of workflow generator scripts, wrapper scripts, Dockerfiles, and README files from a pipeline description to eliminate boilerplate code and reduce setup time.

What is the best way to generate per-sample parallelism patterns in a Pegasus data pipeline?▼

Generating per-sample parallelism patterns in a Pegasus data pipeline is supported through guided configuration prompts that tailor the workflow project structure to your specific data sources, pipeline steps, and tool requirements.

Can I set up API data fetching and ML components in a Pegasus workflow?▼

API data fetching and ML components are supported pipeline patterns in Pegasus workflow generation, allowing you to integrate data retrieval and machine learning steps seamlessly into your automated project structure.

Does Pegasus workflow generation include Docker environments for pipeline tools?▼

Pegasus workflow generation includes Dockerfiles for tool environments, ensuring that each individual pipeline step operates within a containerized setup tailored to your specific tool requirements.

What do I need to configure before generating a Pegasus workflow project?▼

Before generating a Pegasus workflow project, you need to define essential pipeline details such as the pipeline name, execution steps, data sources, parallelism patterns, and tool requirements to tailor the output.

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