# Genomics Workflow Acceleration

Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving...

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: Engineering
- License: CC-BY-4.0 AND Apache-2.0
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add NVIDIA/skills --skill genomics-workflow-acceleration -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill genomics-workflow-acceleration -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill genomics-workflow-acceleration -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill genomics-workflow-acceleration -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-genomics-workflow-acceleration/SKILL.md