pegasus-scaffold

name	pegasus-scaffold
description	Create a complete Pegasus workflow project from a pipeline description
allowed-tools	["Read","Glob","Grep","Write","Edit","Bash"]

Pegasus Workflow Scaffold

You are a Pegasus workflow generator. The user has invoked /pegasus-scaffold to create a new workflow project from scratch.

Step 1: Read Reference Materials

1. Read references/PEGASUS.md from the repository root — this is the comprehensive guide for all Pegasus patterns.
2. Read assets/templates/workflow_generator_template.py — your starting point for the workflow generator.
3. Read assets/templates/wrapper_template.py" and assets/templates/wrapper_template.sh — starting points for wrappers.
4. Read assets/templates/Dockerfile_template — starting point for the container.

Step 2: Gather Requirements

Ask the user the following questions. If they've already provided some answers in their message, skip those.

1. Pipeline name: What should the workflow be called? (e.g., "rnaseq", "weather-analysis")
2. Pipeline steps: Describe each step in order — what tool does it run, what are its inputs and outputs?
3. Data source: Where does input data come from?
   • Local files (FASTQ, CSV, etc.) — needs Replica Catalog entries
   • API fetch at runtime (USGS, OpenAQ, etc.) — first job fetches, no RC entries needed
   • Both (reference files + API data)
4. Iteration pattern: How does the pipeline parallelize?
   • Per-sample (like tnseq: each sample goes through the same pipeline independently)
   • Per-region/location (like earthquake: loop over geographic regions)
   • Single linear pipeline (no parallelism)
   • Fan-out/fan-in (process items in parallel, then merge)
5. Tools needed: List all command-line tools or Python libraries each step uses
6. ML component?: Does the pipeline include model training and/or inference?
   • If yes: train-once-predict-many (hub-and-spoke) or train-per-item?
7. External data directories?: Does the pipeline need access to external data directories at runtime (model caches, databases, reference collections)?
   • If yes → use CondorIO (transfer_input_files) to transfer them to jobs (see Pegasus.md "Transferring Data Directories via CondorIO")
   • Do NOT use container mounts=[] for this — CondorIO is preferred
8. Container preference: pip-based (simple) or micromamba (complex bioinformatics)?
9. Wrapper type: Python wrappers (recommended for most) or shell wrappers (for tools with nested output)?

Step 3: Select Reference Workflow

Based on the user's answers, select the closest existing workflow as a reference pattern:

If the workflow has...	Study this example
Per-sample parallelism, fan-in merge	examples/workflow_generator_tnseq.py
API fetch + region loops	examples/workflow_generator_earthquake.py
Shell wrappers, micromamba, --test mode	examples/workflow_generator_mag.py
ML train-then-predict	examples/workflow_generator_soilmoisture.py
Dual pipeline, skip flags, multiple data sources	examples/workflow_generator_airquality.py
Fork-join topology, complex branching, PLINK bioinformatics	examples/workflow_generator_gwas_qc.py
Nextflow conversion, R support files (edgeR/DESeq2)	examples/workflow_generator_rnaseq.py
CondorIO for caches/databases, GPU jobs, batch inference	examples/workflow_generator_proteinfold.py + Pegasus.md "Transferring Data Directories via CondorIO"
Image tiling, split→parallel→merge, GPU U-Net training	examples/workflow_generator_s2_segmentation.py
Federated learning with SubWorkflows, FL rounds as sub-DAGs	examples/workflow_generator_medical_imaging_fl.py + examples/fl_round.py
Time-window splitting, parallel observation data harvesting	examples/workflow_generator_obs_harvest.py
Hierarchical merge tree, DAGMan rate limiting, inline submit	examples/workflow_generator_sra_search.py

Read the selected reference workflow before generating code.

Step 4: Generate Files

Create the following files in {pipeline-name}-workflow/:

4a. workflow_generator.py

Start from assets/templates/workflow_generator_template.py and customize:

1. Class name: {PipelineName}Workflow
2. wf_name: "{pipeline_name}"
3. __init__: Add pipeline-specific parameters
4. create_transformation_catalog: Register one Transformation per wrapper script with appropriate memory/cores
5. create_replica_catalog: Register input files (or leave empty for API-fetch patterns)
6. create_workflow: Build the DAG with jobs, file objects, and dependencies
7. main(): Add pipeline-specific argparse arguments
8. Input validation: Validate required arguments before any Pegasus API calls

Key rules:

• Use infer_dependencies=True on the Workflow
• Use stage_out=True only on final outputs; stage_out=False for intermediates
• Use register_replica=False on all outputs
• Job _id must be unique — use f"{step}_{item}" pattern
• File objects must be shared between producer and consumer jobs (same Python object, not just same string)
• For fan-in merge steps, collect output files in a list and pass to a merge job via add_inputs(*files)
• For external data directories (caches, databases), use CondorIO transfer_input_files on the Transformation — do NOT use container mounts=[]. Pass os.path.basename() of the directory to wrapper scripts.

4b. bin/{step}.py (one per pipeline step)

Start from assets/templates/wrapper_template.py and customize:

1. argparse arguments: Must exactly match what workflow_generator.py passes in add_args()
2. os.makedirs: Create output subdirectories before writing
3. Tool invocation: Use subprocess.run() for CLI tools, or call Python libraries directly
4. Exit code propagation: sys.exit(result.returncode) after subprocess calls
5. Logging: Print the command being run for debugging

For fan-in merge wrappers, use action="append" or nargs="+" for the input argument.

For shell wrappers (when tools produce nested output), start from assets/templates/wrapper_template.sh.

4c. Docker/{Name}_Dockerfile

Start from assets/templates/Dockerfile_template and customize:

1. Choose base image: python:3.8-slim (pip), mambaorg/micromamba:1.5-jammy (conda), or ubuntu:22.04 (apt+pip)
2. Install all tools needed by all wrapper scripts
3. Set ENV PYTHONUNBUFFERED=1
4. If using shell wrappers with is_stageable=False, COPY bin/*.sh /usr/local/bin/ and chmod +x

4d. README.md

Start from assets/templates/README_template.md and customize with the actual pipeline name, steps, options, and outputs.

4e. run_manual.sh

Start from assets/templates/run_manual_template.sh and customize:

1. Test data download or generation
2. One section per pipeline step, calling the wrapper script with test arguments
3. Output verification after each step

Make the script executable: chmod +x run_manual.sh

Step 5: Validation Checklist

Before presenting the generated code to the user, verify:

• File I/O match: Every add_args() filename matches a File() LFN, and the wrapper's argparse matches
• Dependency chain: File objects are shared between producer/consumer jobs (not duplicated)
• stage_out strategy: Only final outputs have stage_out=True
• Unique job IDs: No duplicate _id values across all jobs
• Replica Catalog completeness: All local input files and support scripts are registered
• Wrapper os.makedirs: Any output path with / has os.makedirs before writing
• Container has all tools: Every tool called by every wrapper is installed in the Dockerfile
• --help works: python3 workflow_generator.py --help would produce useful output
• No directory scanning: No glob(), os.listdir(), or list.files() between jobs
• Support files use os.getcwd(): Not __file__-relative paths

Full Workflow Repositories

For complete working examples beyond the excerpts in examples/:

• https://github.com/pegasus-isi/tnseq-workflow — per-sample bioinformatics, fan-in merge
• https://github.com/pegasus-isi/earthquake-workflow — API data fetch, per-region loops
• https://github.com/pegasus-isi/mag-workflow — shell wrappers, micromamba, metagenomics
• https://github.com/pegasus-isi/soilmoisture-workflow — ML train-then-predict
• https://github.com/pegasus-isi/airquality-workflow — dual pipeline, LSTM forecasting
• https://github.com/pegasus-isi/crophealth-workflow — CNN classification, edge-to-cloud DPU
• https://github.com/pegasus-isi/gwas-qc-workflow — fork-join GWAS QC, PLINK
• https://github.com/pegasus-isi/orcasound-workflow — S3 audio data, per-sensor parallelism
• https://github.com/pegasus-isi/rnaseq-workflow — Nextflow conversion, RNA-Seq, R support files
• https://github.com/pegasus-isi/proteinfold-workflow — GPU protein folding, CondorIO for model caches
• https://github.com/pegasus-isi/s2-segmentation-workflow — Sentinel-2 image tiling, GPU U-Net training
• https://github.com/pegasus-isi/medical-imaging-fl-workflow — federated learning with SubWorkflows
• https://github.com/swarm-workflows/obs-harvest-workflow — parallel observation data harvesting
• https://github.com/pegasus-isi/sra-search-pegasus-workflow — hierarchical merge tree, DAGMan rate limiting