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