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Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows.
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SOC 職業分類に基づく
| name | bio-prefect-dask-nextflow |
| description | Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows. |
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.
| 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 |
sbatch and verifies trace and non-empty result artifactsChoice: Nextflow
Why: CLI-heavy pipeline, HPC scheduler required, reproducible cache/resume needed.
Issue: Workflow fails on HPC due to environment mismatch Solution: Pin container/conda versions and validate with a minimal test dataset.
Review, score, compare, and rank AI-generated biology or bioinformatics research artifacts. Use when auditing AI-scientist notebooks, code, figures, analyses, manuscripts, or reports for rigor, reproducibility, novelty, and task completion.
Search arXiv through its official API and save local Markdown summaries. Use when finding recent CS, math, physics, or quantitative-biology preprints or resolving arXiv IDs.
Create publication-quality static charts with matplotlib or seaborn. Use when scientific figures need readable axes, accessible palettes, tight layouts, and high data-ink design.
Annotate genes or proteins and infer taxonomy from sequence homology. Use when assigning functions, domains, or taxonomic labels to genomes, contigs, or protein sets.
Assemble genomes or metagenomes and assess assembly quality. Use when turning sequence reads into contigs and reporting completeness, continuity, and contamination evidence.
Bin and refine metagenomic contigs, then assess MAG quality. Use when recovering genomes with QuickBin and checking completeness, contamination, and bin consistency.