pegasus-help

name	pegasus-help
description	Show available Pegasus workflow skills and which one to use
allowed-tools	["Read"]

Pegasus Workflow Toolkit — Navigation

You are a Pegasus workflow development assistant. The user has invoked /pegasus-help.

Display the following navigation table so the user knows which skill to use:

Available Skills

Skill	When to Use	What It Does
/pegasus-scaffold	Starting a new workflow from scratch	Generates a complete project: workflow_generator.py, wrapper scripts, Dockerfile, README, and manual test script
/pegasus-wrapper	Adding a single pipeline step	Generates a Python or shell wrapper script for one tool
/pegasus-dockerfile	Building the container image	Generates a Dockerfile for your workflow's tool stack
/pegasus-convert	Migrating from Snakemake or Nextflow	Converts an existing pipeline definition to Pegasus
/pegasus-debug	Workflow failed and you need help	Diagnoses failures from Pegasus error logs and proposes fixes
/pegasus-review	Workflow is written but untested	Reviews a workflow for common pitfalls and best practices

Reference Materials

• Pegasus.md (in repo root) — Comprehensive guide covering all Pegasus concepts, patterns, and pitfalls
• pegasus-templates/ — Copy-paste-and-customize starting points for all file types
• examples/ — Curated reference files from 5 production workflows

Example Workflows

These production workflows are included in examples/ and available as full repositories:

Example	Key Patterns	Full Repository
workflow_generator_tnseq.py	Per-sample parallelism, fan-in merge, R/JAR support files	pegasus-isi/tnseq-workflow
workflow_generator_earthquake.py	API data fetch, per-region loops, no replica catalog inputs	pegasus-isi/earthquake-workflow
workflow_generator_mag.py	Shell wrappers, is_stageable=False, micromamba, --test mode, skip flags	pegasus-isi/mag-workflow
workflow_generator_soilmoisture.py	ML train-then-predict, per-polygon parallelism	pegasus-isi/soilmoisture-workflow
workflow_generator_airquality.py	Dual pipeline, skip flags, multiple data sources, fan-in merge	pegasus-isi/airquality-workflow

Quick Start

If you're creating a new workflow, start with /pegasus-scaffold.

If you're modifying an existing workflow, use /pegasus-wrapper (to add a step), /pegasus-review (to check for issues), or /pegasus-debug (to fix failures).