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).