bio-prefect-dask-nextflowlisted

# 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 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 ```text Choice: Nextflow Why: CLI-heavy pipeline, HPC scheduler required, re