bio-prefect-dask-nextflow
Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-prefect-dask-nextflow --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 ```tex
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Engine recommendation
- Troubleshooting
What does the bio-prefect-dask-nextflow skill do?
Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-prefect-dask-nextflow --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.