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Show available Pegasus workflow skills and which one to use
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Convert a Snakemake or Nextflow pipeline to a Pegasus workflow
Generate a Dockerfile for a Pegasus workflow's tool stack
Review a Pegasus workflow for common pitfalls and best practices
Create a complete Pegasus workflow project from a pipeline description
Diagnose Pegasus workflow failures from error messages and logs
Generate a wrapper script for a single Pegasus pipeline step
| name | pegasus-help |
| description | Show available Pegasus workflow skills and which one to use |
| allowed-tools | ["Read"] |
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:
| 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 |
Pegasus.md (in repo root) — Comprehensive guide covering all Pegasus concepts, patterns, and pitfallspegasus-templates/ — Copy-paste-and-customize starting points for all file typesexamples/ — Curated reference files from 5 production workflowsThese 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 |
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).