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Bio prefect dask nextflow

Skill BioTender-max/awesome-bio-agent-skills/skills/omics/bio-prefect-dask-nextflow

Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.From its SKILL.md

Install
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill bio-prefect-dask-nextflow

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

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  • no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.

SKILL.md

1.6 KB, 346 tokens by cl100k_base, as published. Nobody here has run it

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

TaskAction
Engine choiceSee decision-matrix.md
Prefect+Dask scaffoldSee prefect-dask.md
Prefect on SlurmSee prefect-hpc-slurm.md
Nextflow on HPCSee nextflow-hpc.md
ExamplesSee 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.

What ships with it: 5 files

11.7 KB alongside SKILL.md

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