pegasus-wrapper

Generate Python or shell wrapper scripts for Pegasus workflow pipeline steps.

Updated Feb 11, 2026

Search Tags:#workflow #devops #script generation #pipeline #wrapper #pegasus

Ready to run

npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-wrapper

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pegasus-wrapper
Source: https://github.com/pegasus-isi/pegasus-workflow-toolkit/tree/main/.claude/skills/pegasus-wrapper
Command: npx skills add https://github.com/pegasus-isi/pegasus-workflow-toolkit --skill pegasus-wrapper

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the creation of wrapper scripts for individual pipeline steps within Pegasus workflows, ensuring consistency and reducing manual coding errors.

Core Features & Use Cases

Wrapper Script Generation: Creates Python or shell scripts to encapsulate single tool executions.
Input/Output Handling: Guides the user to define tool inputs, outputs, and nested directory structures.
Use Case: You need to create a wrapper for samtools sort to process BAM files. This Skill will help you define the input BAM, output sorted BAM, and ensure the command is correctly formatted for Pegasus.

Quick Start

Use the pegasus-wrapper skill to generate a Python wrapper for the 'bwa mem' tool.

Frequently Asked Questions about pegasus-wrapper

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

FAQPage Schema

How do I generate wrapper scripts for Pegasus workflow pipeline steps?▼

To generate wrapper scripts for Pegasus workflow pipeline steps, use this Skill to automate the creation of Python or shell scripts that encapsulate individual tool executions. It automatically defines tool invocations, argument parsing, and input/output handling for deterministic execution.

What is a Pegasus wrapper script and when do I need one?▼

A Pegasus wrapper script is a Python or shell script that encapsulates a single tool execution within a workflow pipeline. You need one to ensure synchronization between tool invocations and workflow generator configurations, which reduces manual coding errors and guarantees deterministic execution.

How do I handle input and output file staging for Pegasus wrapper scripts?▼

You handle input and output file staging for Pegasus wrapper scripts by using this Skill to guide the definition of tool inputs, outputs, and nested directory structures. It automates the support file staging required for individual workflow pipeline steps.

Can I create shell wrappers for bioinformatics tools like samtools sort in Pegasus?▼

Yes, you can create shell or Python wrappers for bioinformatics tools like samtools sort in Pegasus. The Skill helps you define the input BAM, output sorted BAM, and ensures the command is correctly formatted for the workflow pipeline.

Does the pegasus-wrapper skill synchronize wrapper scripts with workflow generator configurations?▼

Yes, the pegasus-wrapper skill ensures synchronization between wrapper scripts and workflow generator configurations. This guarantees that individual pipeline step executions remain deterministic and consistent with the overall Pegasus workflow definition.

What is the best way to automate argument parsing for Pegasus pipeline tool invocations?▼

The best way to automate argument parsing for Pegasus pipeline tool invocations is to generate wrapper scripts using this Skill. It automatically defines the argument parsing and tool invocation logic to ensure consistent and error-free command execution.