Bio Prefect + Dask + Nextflow

This skill helps an agent design, scaffold, and harden bioinformatics pipelines across:

• Local workstation/laptop (Prefect + Dask LocalCluster)
• HPC clusters (Nextflow executors; or Prefect → Slurm worker patterns)
• Hybrid patterns (Prefect orchestrates metadata/approvals/notifications; Nextflow runs heavy compute)

Use this skill when

• The user mentions Prefect, Dask, Nextflow, HPC, Slurm, PBS, nf-core, or “bioinformatics pipeline”.
• The user needs parallelism, distributed execution, retries, scheduling, reproducible runs, or “local prototype then scale”.

Outputs this skill should produce

When activated, the agent should return (and/or generate in a repo):

1. Engine choice: prefect+dask, nextflow, or hybrid, with rationale.
2. Runnable scaffold (files + commands) for the chosen engine.
3. Resource plan per step (cpus/mem/time) + I/O layout (scratch vs shared).
4. Validation plan: tiny test run + failure/retry + resume test.
5. Pitfalls & mitigations: what will likely break on HPC and why.

2-minute decision

Use the decision matrix for nuance: decision-matrix.md

Default heuristics:

• Choose Nextflow if the pipeline is mainly CLI tools over files, must run on HPC schedulers, and reproducibility/caching are top priorities.
• Choose Prefect + Dask if the pipeline is mainly Python functions, needs dynamic branching, API/DB integration, or interactive development.
• Choose Hybrid if Prefect should own the “outer loop” (metadata, batching, approvals, notifications) while Nextflow owns “inner loop” compute.

Standard workflow (agent playbook)

1. Requirements intake
   • Scheduler type (Slurm/PBS/LSF/etc), queue/partition rules, walltime limits, node topology.
   • Container policy (Docker vs Singularity/Apptainer vs no containers) and module/conda availability.
   • Data location and throughput constraints (shared FS vs scratch, object storage).
   • Parallelism shape (many independent samples? big distributed arrays? long single jobs?).
2. Choose engine using decision-matrix.md; state assumptions.
3. Scaffold the project
   • Prefect path → prefect-dask.md and (if needed) prefect-hpc-slurm.md
   • Nextflow path → nextflow-hpc.md
4. Implement steps with replayable boundaries
   • Each step idempotent; deterministic output paths.
   • Pass around paths/URIs, not giant in-memory objects.
5. Add operational glue
   • Logging, retries/timeouts, resource hints, output manifest.
6. Validate locally
   • Tiny dataset run + forced failure + resume/retry test.
7. Scale to HPC
   • Confirm filesystem layout, job submission permissions, and environment bootstrap.

Response template

Use this template in your final answer to the user:

# Pipeline plan: [name]

## Recommended engine
- Choice: [prefect+dask | nextflow | hybrid]
- Why: [3–6 bullet rationale]

## Project scaffold
- Files to create:
  - ...
- Commands to run:
  - ...

## Execution model
- Parallelism strategy:
- Resource plan (per step):
- Data layout (work/results/cache):

## Pitfalls & mitigations
- ...

## Validation checklist
- ...

Deep references (read as needed)

• Engine comparison and “when to use what”: decision-matrix.md
• Prefect + Dask local patterns: prefect-dask.md
• Prefect on Slurm + Dask-on-HPC options: prefect-hpc-slurm.md
• Nextflow on HPC (executors, modules, resume/cache): nextflow-hpc.md
• Examples (Prefect-only, Nextflow-only, Hybrid): examples.md
• Validation loop + common failure modes: validation-checklist.md