pegasus-convert

What problem does it solve?

This Skill automates the complex and time-consuming process of converting existing Snakemake or Nextflow data processing pipelines into the Pegasus workflow management system.

Core Features & Use Cases

• Automated Conversion: Translates pipeline logic, inputs, outputs, and commands from other workflow languages into Pegasus transformations, jobs, and wrapper scripts.
• Concept Mapping: Provides explicit mappings for common constructs like rules, processes, inputs, outputs, shell commands, and resource definitions.
• Use Case: A bioinformatics lab has a well-established Snakemake pipeline for genomic analysis. They need to migrate this to a high-performance computing environment that uses Pegasus. This Skill will convert their Snakefile and associated scripts into a functional Pegasus workflow generator.

Quick Start

Use the pegasus-convert skill to convert the attached Snakefile and its associated configuration files into a Pegasus workflow.