Bio Prefect + Dask + Nextflow

Choose and scaffold the right workflow engine for local, distributed, or HPC bioinformatics pipelines.

Instructions

1. Collect requirements (scheduler, container policy, data location, scale).
2. Choose engine: Prefect+Dask, Nextflow, or Hybrid.
3. Generate a runnable scaffold with clear data layout and resources.
4. Validate with a small test and resume/retry checks.

Quick Reference

Task	Action
Engine choice	See decision-matrix.md
Prefect+Dask scaffold	See prefect-dask.md
Prefect on Slurm	See prefect-hpc-slurm.md
Nextflow on HPC	See nextflow-hpc.md
Examples	See examples.md

Input Requirements

• Workflow requirements and steps
• Target environment (local, cluster, cloud)
• Scheduler and container constraints
• Data locations and expected volumes

Output

• Engine recommendation with rationale
• Runnable scaffold (files + commands)
• Resource plan per step
• Validation plan and checkpoints

Quality Gates

• Tiny test run completes end-to-end
• Resume/retry behavior verified
• Resource plan matches cluster limits

Examples

Example 1: Engine recommendation

Choice: Nextflow
Why: CLI-heavy pipeline, HPC scheduler required, reproducible cache/resume needed.

Troubleshooting

Issue: Workflow fails on HPC due to environment mismatch Solution: Pin container/conda versions and validate with a minimal test dataset.