Versioned security assessment

Report ID: SA-B5C8DF98

6/30/2026, 5:52:40 AM

dnanexus-integration security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
dnanexus-integration
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/dnanexus-integration
Coverage
6 Files scanned · 2,616 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Medium

1 confirmed security finding requires attention.

Installation context

Historical evidence

This report may not describe the currently installable artifact. Open the current Skill page for install guidance.

Open current Skill page

This report does not block or authorize the manifest or ZIP.

Static analysis reported many command, weak-crypto, reconnaissance, and sensitive-data patterns, but most are false positives from Markdown examples and DNAnexus terminology. Human review found no prompt injection or confirmed malicious intent, but the skill legitimately guides authenticated cloud data movement, external commands, Docker, network access, project permissions, and destructive operations. Publish with warnings and require user confirmation for credentials, data movement, job execution, and removal actions.

Report position

Historical report

Open audit history before using this report to install.

Audit attestation

Not attestable

The required immutable binding is incomplete.

Human verification

Not verified

No human verification is recorded for this report.

Coverage

6 Files scanned · 2,616 Lines analyzed

6 items shown for review

Limitations

This report does not claim runtime or sandbox execution and does not prove the absence of side effects.

Evidence chain

Follow the evidence from source binding to the install contract. Available evidence supports verification; it is not a safety guarantee.

  1. Source

    Binding unavailable

  2. Artifact

    Identity incomplete

  3. Audit

    Complete

  4. Install contract

    Open manifest to verify

    Open manifest

Capabilities observed

Observed means this report recorded supporting evidence. Not recorded does not prove that a capability is absent.

Contains scripts

May execute code included with the Skill.

Not recorded by this audit

Network access

May connect to external services.

Observed in 3 evidence locations

Filesystem access

May read or write local files.

Observed in 4 evidence locations

Env variables

May read values from the process environment.

Observed in 2 evidence locations

External commands

May invoke commands or programs outside the Skill.

Observed in 4 evidence locations

Capability review items (5)
Medium
SKILL.md:158-176references/data-operations.md:58-78references/data-operations.md:90-111references/data-operations.md:225-231
Authenticated DNAnexus Data Movement
TRUE POSITIVE for operational risk: the skill teaches upload, download, search, and result retrieval patterns for authenticated DNAnexus projects. This is legitimate for the skill purpose, but mishandled prompts could move regulated genomics data or write results to the wrong project.
The cited examples directly describe cloud file upload, download, and searches across accessible projects. The use is expected for DNAnexus, but the data sensitivity and project scope create real operational risk.
Medium
SKILL.md:204-220references/app-development.md:115-127references/configuration.md:294-309references/configuration.md:406-419
External Command Execution Guidance
PARTIAL TRUE POSITIVE: most static Ruby/backtick alerts are false positives caused by Markdown code fences, but the skill does include shell, subprocess, dx CLI, pip, and Docker execution examples. Commands appear instructional rather than malicious, but execution should require review.
The files are Markdown documentation, not executable scripts, which lowers malicious confidence. The command and subprocess examples are real and could affect local files, packages, containers, or cloud jobs if executed automatically.
Medium
references/configuration.md:406-419references/configuration.md:440-452references/configuration.md:567-568references/configuration.md:591
Broad Network and Docker Permission Examples
TRUE POSITIVE for elevated platform risk: configuration examples include Docker execution and broad network access. These are common in bioinformatics workflows, but they increase supply-chain, egress, and reproducibility risks.
The examples explicitly request network access and run Docker containers. The same document also advises limiting network permissions, so this is a legitimate but review-worthy pattern.
Low
SKILL.md:377-379
Hardcoded Documentation URLs
TRUE POSITIVE but low risk: the skill lists DNAnexus documentation, API reference, and GitHub URLs. They are transparent reference links, not hidden exfiltration endpoints.
The URLs are visible documentation resources and match the skill topic. No evidence found of credential or data submission to these links.
Low
references/python-sdk.md:28-44references/python-sdk.md:451-457
API Token Handling Examples Use Placeholders
LOW RISK: the Python SDK reference shows token configuration with placeholder values and also warns against hardcoding tokens. Users still need guidance to avoid pasting real tokens into generated files.
The token examples use placeholders, which reduces immediate risk. The pattern is still sensitive because environment-based authentication can expose secrets if copied into logs or source files.

Risk findings

Confirmed security concerns are separated from items that still need review.

Confirmed security concerns (1)

RISK-001 Medium
references/data-operations.md:275-285references/data-operations.md:319-330references/python-sdk.md:324-337references/job-execution.md:310-320
Project Permission and Destructive Operation Guidance
TRUE POSITIVE for sensitive capability: the references document project invitations, file removal, permanent deletion, and job termination. These are valid DNAnexus operations, but they require explicit user confirmation and least-privilege checks.
The cited lines directly cover sharing, removal, deletion, and termination APIs. They are legitimate administrative examples but can cause data loss, access changes, or interrupted analysis.

Expert evidence

Immutable subject identity, scanner metadata, dismissed matches, and source-level evidence.

Artifact subject

Marketplace commit
Unavailable
Content hash
Unavailable
Tree hash
Unavailable
Skill path
Unavailable
Audit payload hash
Unavailable

Analysis metadata

Audit model: codex

Analysis state: Complete

Scope is limited to the recorded files, lines, methods, and evidence. No runtime or sandbox execution is claimed.

Static false positives ignored (1)
Low
references/configuration.md:106-116SKILL.md:270-275references/python-sdk.md:419-428
Static Weak-Crypto and Reconnaissance Alerts Are Mostly False Positives
FALSE POSITIVE: scanner hits for weak cryptography and reconnaissance appear to come from DNAnexus terms such as hash input type, object describe methods, and whoami/version checks. No evidence found of cryptographic implementation, password dumping, or host reconnaissance intent.
The suspicious terms are ordinary DNAnexus documentation and introspection examples. I did not find evidence that the skill implements MD5/SHA1 hashing, dumps Windows SAM data, or performs host reconnaissance.

Verify and export

JSON report CITATION.cff SARIF 2.1.0 Signed installation manifest

The manifest and lockfile bind install artifacts to cryptographic hashes. This integrity claim is separate from the security assessment.

Audit attestation: not_attestable