Sign Parabricks skill by ohadmo · Pull Request #51 · NVIDIA-BioNeMo/bionemo-agent-toolkit

ohadmo · 2026-10-02T00:05:03Z

No description provided.

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T00:05:10Z

@greptileai

ohadmo · 2026-10-02T00:05:17Z

/nvskills-ci

greptile-apps · 2026-10-02T00:07:07Z

Confidence Score: 5/5

[Medium impact] The changes since the last review appear safe to merge.

Summary

Updates the Parabricks skill to version 1.3.0 with clearer command guidance, STAR translation, runtime checks, and expanded evaluations.

The Parabricks skill plans individual commands from supplied details.
STAR arguments can become reviewable Parabricks RNA command drafts.
Operators can check Parabricks readiness without launching containers by default.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart TD
  A[Readiness request] --> B{Entry point}
  B -->|Python compatibility entry| C[Start Bash helper]
  B -->|Bash| D[Check arguments and timeout utility]
  C --> D
  D --> E[Inspect host and requested storage]
  E --> F{Container probes authorized?}
  F -->|Yes| G[Probe selected images]
  F -->|No| H[Leave container checks unverified]
  G --> I[Return text or JSON report]
  H --> I

_{Reviews (25) · Last reviewed commit: "Fix Parabricks Tier 1 scan coverage and ..." · Reviewed by Greptile}

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T00:56:56Z

/nvskills-ci

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T01:22:42Z

/nvskills-ci

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T17:45:41Z

/nvskills-ci

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T18:39:31Z

/nvskills-ci

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T18:57:00Z

/nvskills-ci

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T21:37:57Z

/nvskills-ci

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-02T22:09:58Z

/nvskills-ci

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-07T18:17:38Z

/nvskills-ci

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

- Update tool references and command conventions for Parabricks 4.7.1 - Improve planning triggers, option translation, and input safeguards - Replace the Python readiness helper and adapt tests and eval fixtures Signed-off-by: Angel Pizarro <apizarro@nvidia.com>

…s-skill Signed-off-by: Angel Pizarro <apizarro@nvidia.com>

ohadmo · 2026-10-12T19:06:35Z

/nvskills-ci

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-12T19:36:09Z

/nvskills-ci

Restore genomics-workflow-acceleration source metadata and readiness guidance to the main branch versions. Those changes are now handled in a separate PR, so this branch should validate only the Parabricks skill. Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-12T23:25:10Z

/nvskills-ci

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-13T17:24:42Z

/nvskills-ci

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo · 2026-10-13T22:02:27Z

/nvskills-ci

ohadmo · 2026-10-13T22:39:35Z

/nvskills-ci

ohadmo · 2026-10-13T23:02:33Z

/nvskills-ci

Sign Parabricks skill

a646daa

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

Deduplicate Parabricks skill references and fix CI validation issues

1208967

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

Attach NVSkills validation signatures

9875a9b

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

greptile-apps Bot reviewed Oct 2, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/parabricks/skill-card.md Outdated

Clarify Parabricks runtime requirements and NGC authentication

e2fadf2

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

greptile-apps Bot reviewed Oct 2, 2026

View reviewed changes

Comment thread skills/bionemo-agent-toolkit/skills/parabricks/SKILL.md

Comment thread library-skills/parabricks/SKILL.md Outdated

Attach NVSkills validation signatures

960ad38

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

greptile-apps Bot reviewed Oct 2, 2026

View reviewed changes

Comment thread skills/bionemo-agent-toolkit/skills/parabricks/BENCHMARK.md Outdated

Fix Parabricks GPU detection and improve skill evaluation

d08cf9a

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

greptile-apps Bot reviewed Oct 2, 2026

View reviewed changes

Comment thread library-skills/parabricks/evals/evals.json Outdated

Comment thread library-skills/parabricks/references/runtime-environment.md

Attach NVSkills validation signatures

254203a

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

greptile-apps Bot reviewed Oct 2, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/parabricks/skill-card.md Outdated

Fix truncated dataset digests in generated skill cards

d813c47

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

greptile-apps Bot reviewed Oct 2, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/parabricks/skill-card.md Outdated

Document release-compatible CUDA probes for Parabricks 4.2

1494369

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo force-pushed the parabricks-skill branch from 9daa040 to 1494369 Compare October 2, 2026 18:56

greptile-apps Bot reviewed Oct 2, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/parabricks/skill.oms.sig Outdated

svc-nvskills-signing and others added 2 commits October 2, 2026 19:07

Attach NVSkills validation signatures

5308876

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

Avoid sensitive host probes in Parabricks readiness checks

60fede8

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

Fix Parabricks Tier 1 false positive in Docker socket guidance

53b7d6e

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

svc-nvskills-signing and others added 2 commits October 2, 2026 22:22

Attach NVSkills validation signatures

e5c239f

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

Add STAR translation helper and strengthen Parabricks evaluations

159fa23

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo force-pushed the parabricks-skill branch from e5c239f to 159fa23 Compare October 7, 2026 18:16

greptile-apps Bot reviewed Oct 7, 2026

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Comment thread library-skills/parabricks/scripts/translate_star_to_parabricks.py Outdated

Comment thread skills/bionemo-agent-toolkit/skills/parabricks/skill-card.md Outdated

Comment thread skills/bionemo-agent-toolkit/skills/parabricks/BENCHMARK.md Outdated

Attach NVSkills validation signatures

689e4e3

Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>

greptile-apps Bot reviewed Oct 7, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/parabricks/BENCHMARK.md Outdated

delagoya added 2 commits October 8, 2026 13:18

Merge remote-tracking branch 'origin/parabricks-skill' into parabrick…

b92e22f

…s-skill Signed-off-by: Angel Pizarro <apizarro@nvidia.com>

greptile-apps Bot reviewed Oct 8, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/parabricks/parabricks/SKILL.md Outdated

Comment thread library-skills/parabricks/scripts/check_parabricks_runtime.sh Outdated

Comment thread skills/bionemo-agent-toolkit/skills/parabricks/BENCHMARK.md Outdated

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remove nested skill and sync generated payload

9aefbf0

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

greptile-apps Bot reviewed Oct 12, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/parabricks/references/pbrun-deepvariant.md

Comment thread skills/bionemo-agent-toolkit/skills/parabricks/references/pbrun-haplotypecaller.md

Comment thread skills/bionemo-agent-toolkit/skills/parabricks/references/pbrun-rna_fq2bam.md

greptile-apps Bot reviewed Oct 12, 2026

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Comment thread skills/bionemo-agent-toolkit/skills/genomics-workflow-acceleration/skill-card.md Outdated

ohadmo force-pushed the parabricks-skill branch from 18114c6 to 3dfcba8 Compare October 12, 2026 22:08

greptile-apps Bot reviewed Oct 12, 2026

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Comment thread library-skills/parabricks/references/shared-options.md Outdated

add Instructions and Examples section headings

a8be2ea

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

Improve Parabricks command guidance and reduce duplicated skill context

164315c

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>

ohadmo force-pushed the parabricks-skill branch from 9af813b to 164315c Compare October 13, 2026 22:02

greptile-apps Bot reviewed Oct 13, 2026

View reviewed changes

Comment thread library-skills/parabricks/scripts/check_parabricks_runtime.sh

Fix Parabricks review findings and stale publication metadata

613948e

Fix Parabricks Tier 1 scan coverage and runtime validation

d70b327

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Confidence Score: 5/5

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Diagram

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