Agent skill · nvidia
genomics-workflow-acceleration
Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs, or comparing CPU and GPU workflow outputs. Adds optional GPU steps in-place with runtime toggles (default off). Do NOT use for individual pbrun command routing — use parabricks.
What it needs
About 7k tokens when loaded.
What this skill does
Genomics workflow acceleration Purpose Inspect an existing genomics workflow, map CPU steps to NVIDIA Parabricks, and add optional GPU-accelerated steps in place alongside the original CPU steps. Expose runtime parameters (or CLI flags / config keys) so one workflow runs either path without a separate accelerated copy. Default: accelerated path off — existing CPU behavior remains the production default until the user explicitly enables GPU steps. Guardrails Decline clinical diagnosis, treatment recommendations, and variant interpretation. Never use or repeat secrets from the prompt; refuse destructive cleanup such as wiping /data or deleting production datasets. Do not invent pipeline structure, sample names, paths, or container tags. Do not claim bit-identical VCF/BAM output without a comparison run. Do not claim Parabricks runs on CPU. Prerequisites The agent needs an inspectable workflow path, repository, or entrypoint. Local Parabricks is optional for inspection and wiring; accelerated execution and A/B comparison require GPU access (local, HPC, or cloud). Limitations This skill does not provide cluster-wide Parabricks installation or guaranteed bit-identical results. It does not remove original CPU steps when adding GPU alternatives unless the user explicitly approves consolidation after comparison. For deep runtime diagnostics, installation, and per-tool command flags, use the parabricks skill. References parabricks-runtime-readiness.md — local check; HPC/cloud guidance workflow-frameworks.md — detect framework; in-place patterns parabricks-tool-map.md — CPU → Parabricks mapping (all frameworks) nf-core-parabricks-map.md — Nextflow nf-core modules workflow-layout.md — toggle naming, layout, ACCELERATION.md step-consolidation.md — merge steps on GPU branch comparison-checklist.md — toggle-off vs toggle-on validation Instructions 1. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills nvidia/bionemo-genomics-workflow-acceleration