fmschulz Bio Prefect + Dask + Nextflow
Choose and scaffold the right workflow engine for local, distributed, or HPC bioinformatics pipelines.
Supplementary docs last verified: 2026-05-30. Current source checks cover Prefect 3.7.2, Dask/distributed 2026.3.0, prefect-dask v0.2.6 (archived repository; install through prefect[dask]), and Nextflow v26.04.3.
Instructions
- Collect requirements (scheduler, container policy, data location, scale).
- Choose engine: Prefect+Dask, Nextflow, or Hybrid.
- Generate a runnable scaffold with clear data layout and resources.
- 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 |
| Submit Nextflow through Slurm | SLURM_ACCOUNT=... scripts/submit_nextflow.sh main.nf 'data/*.fastq.gz' results |
| 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
- Temporary Dask clusters are created by the task runner at flow runtime and closed with the flow
- Compound FASTQ suffixes do not leak into sample output names
- Nextflow launch runs through
sbatchand verifies trace and non-empty result artifacts
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.