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pegasus-wrapper

Official

Generate Pegasus wrapper scripts

Software Engineering#workflow#devops#script generation#pipeline#wrapper#pegasus
Authorpegasus-isi
Version1.0.0
Installs0

System Documentation

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.

Dependency Matrix

Required Modules

None required

Components

scriptsreferences

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: pegasus-wrapper
Download link: https://github.com/pegasus-isi/pegasus-workflow-toolkit/archive/main.zip#pegasus-wrapper

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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