# Pegasus Help > Show available Pegasus workflow skills and which one to use Use when this capability is needed. - Skill: `tomevault-io/pegasus-help` (Agent Skill, multi-file: 2 files) - Install (CLI): `npx skillmds@latest add tomevault-io/pegasus-help` - Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/pegasus-help/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Productivity - Author: tomevault-io (https://skillmd.com/u/tomevault-io) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/tomevault-io/pegasus-help --- # 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 - **`references/PEGASUS.md`** (in repo root) — Comprehensive guide covering all Pegasus concepts, patterns, and pitfalls - **`assets/templates/`** — Copy-paste-and-customize starting points for all file types - **`assets/examples/`** — Curated reference files from 5 production workflows ## Example Workflows These production workflows are included in `assets/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](https://github.com/pegasus-isi/tnseq-workflow) | | `workflow_generator_earthquake.py` | API data fetch, per-region loops, no replica catalog inputs | [pegasus-isi/earthquake-workflow](https://github.com/pegasus-isi/earthquake-workflow) | | `workflow_generator_mag.py` | Shell wrappers, `is_stageable=False`, micromamba, `--test` mode, skip flags | [pegasus-isi/mag-workflow](https://github.com/pegasus-isi/mag-workflow) | | `workflow_generator_soilmoisture.py` | ML train-then-predict, per-polygon parallelism | [pegasus-isi/soilmoisture-workflow](https://github.com/pegasus-isi/soilmoisture-workflow) | | `workflow_generator_airquality.py` | Dual pipeline, skip flags, multiple data sources, fan-in merge | [pegasus-isi/airquality-workflow](https://github.com/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). --- > Converted and distributed by [TomeVault](https://tomevault.io/claim/pegasus-isi) — claim your Tome and manage your conversions.