Does this skill help with environment reproducibility?

Absolutely. It analyzes conda: YAML files or container directives to create a Dockerfile that includes all necessary tools for the workflow to run consistently across different infrastructures.

How does it handle Snakemake wildcards?

The skill converts Snakemake wildcards, such as {sample}, into explicit Python loops and list comprehensions within the Pegasus workflow generator for more predictable job scheduling.

What happens to shell commands in the original pipeline?

Each shell command is extracted and placed into a dedicated Python wrapper script in the bin/ directory, which Pegasus then executes as a job.

Can it convert Nextflow processes that use containers?

Yes, it identifies container directives in Nextflow and maps them to Pegasus Transformation Catalog entries, including the generation of a corresponding Dockerfile.

Does it support complex data dependencies like Nextflow channels?

It maps Nextflow channel operations to standard Python data structures and Pegasus file objects, ensuring that data flow and dependencies remain intact during migration.

Pegasus Workflow Converter

Name: Pegasus Workflow Converter
Author: pegasus-isi

bypegasus-isi

0•

데이터 과학 및 ML

Converts Snakemake and Nextflow pipelines into robust Pegasus workflows for high-performance computing environments.

The pegasus-convert skill automates the migration of scientific pipelines from Snakemake or Nextflow to the Pegasus Workflow Management System. It intelligently maps pipeline rules and processes to Pegasus transformations and jobs, handles wildcard mapping via Python loops, and generates necessary wrapper scripts and Dockerfiles. This tool is essential for researchers and data scientists looking to scale their local bioinformatics or data analysis pipelines to distributed grid, cloud, or HPC infrastructures while maintaining environment reproducibility and fault tolerance.

주요 기능

010 GitHub stars

02Side-by-side conversion reporting for verification and validation

03Automatic mapping of Snakemake rules and Nextflow processes to Pegasus Transformations

04Automated Dockerfile generation from Conda environments or container directives

05Converts pipeline wildcards and channels into scalable Python loop structures

06Generates Python-based workflow_generator.py and bin wrapper scripts

사용 사례

01Migrating local bioinformatics pipelines from Snakemake to distributed HPC environments

02Scaling Nextflow data processing tasks to leverage Pegasus's advanced data management

03Standardizing heterogeneous scientific workflows into a unified, reproducible Pegasus architecture

What are Skills?·How to Install

Install with 🐟 Skill.Fish

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

For use in Claude.ai and ChatGPT

Download Skill