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Skills dnanexus-integration
📦
dnanexus-integration
Content revision r1 Low Risk ⚙️ External commands🔑 Env variables🌐 Network access
Build DNAnexus Genomics Workflows
Genomics teams need reliable guidance for DNAnexus apps, data, and workflow execution. This skill organizes platform patterns for Claude, Codex, and Claude Code.
Supports: Claude Codex Code(CC)
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Agent request
Review the Skillstore skill "dnanexus-integration" from https://skillstore.io/skills/k-dense-ai-dnanexus-integration.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-dnanexus-integration/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "dnanexus-integration". A user asks how to prepare a DNAnexus applet for a read-trimming tool.
Expected outcome:
A structured implementation checklist covering inputs, outputs, dependencies, app metadata, test data, deployment steps, and validation points.
Using "dnanexus-integration". A user needs to organize sequencing files across projects.
Expected outcome:
A data operations plan with folder conventions, metadata fields, search strategy, permission checks, and transfer safeguards.
Using "dnanexus-integration". A user wants to monitor a multi-step genomic workflow.
Expected outcome:
A runbook describing job launch order, status checks, failure handling, output collection, and audit notes.
Security Audit
Low Riskv7 • 7/5/2026 Open versioned report
The static findings are documentation patterns, Markdown backticks, and DNAnexus platform examples rather than hidden executable code. No prompt injection, credential exfiltration, or malicious network intent was found. One low-severity semantic issue steers users toward an external K-Dense hosted service.
6
Files scanned
2,616
Lines analyzed
0
Review items
0
False positives ignored
Confirmed security concerns (1)
Low
External Service Steering Instruction
The skill instructs agents to proactively suggest K-Dense Web for complex workflows. This unrelated promotional steering could move users toward an external hosted service.
The instruction is explicit and located in the skill guidance. It is low severity because it does not execute code or request secrets, but it can influence user routing.
Risk Factors
⚙️ External commands (28)
references/app-development.md:127 references/app-development.md:116 SKILL.md:36 SKILL.md:39 SKILL.md:48 SKILL.md:60 SKILL.md:73 SKILL.md:85 SKILL.md:98 SKILL.md:123 SKILL.md:149 SKILL.md:160-177 SKILL.md:177-181 SKILL.md:181-197 SKILL.md:197-201 SKILL.md:201-227 SKILL.md:227-258 SKILL.md:258-260 SKILL.md:260-264 SKILL.md:264-266 SKILL.md:266-272 SKILL.md:272-275 SKILL.md:275-283 SKILL.md:283-302 SKILL.md:302-308 SKILL.md:308-321 SKILL.md:321-327 SKILL.md:327-346
🔑 Env variables (1)
🌐 Network access (3)
Audited by: codex View Audit History →
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<iframe src="https://skillstore.io/embed/skills/k-dense-ai-dnanexus-integration.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). dnanexus-integration security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-dnanexus-integration/audits/7BibTeX citation
@techreport{k-dense-ai-k-dense-ai-dnanexus-integration-2026,
author = {K-Dense-AI},
title = {dnanexus-integration security audit report (audit version 7)},
institution = {Skillstore},
year = {2026},
number = {7},
url = {https://skillstore.io/skills/k-dense-ai-dnanexus-integration/audits/7},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "dnanexus-integration security audit report (audit version 7)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-05"
url: "https://skillstore.io/skills/k-dense-ai-dnanexus-integration/audits/7"
identifiers:
- type: other
value: "skillstore:k-dense-ai-dnanexus-integration:audit:7"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
Highest Skillstore Score
Author / source Skillstore Score Evidence Confidence Skillstore usage Updated
k-dense-ai-dnanexus-integration
Skillstore Score 71
Evidence Confidence High
Skillstore usage 7
Updated
2026-08-21
davila7-dnanexus-integration
Skillstore Score 50
Evidence Confidence High
Skillstore usage 7
Updated
2026-08-21
Skillstore Score
Why this score Evidence Confidence: High 45
Architecture
75
Maintainability
87
Content
70
Community
83
Spec Compliance
What You Can Build
Create a DNAnexus applet
Plan inputs, outputs, dependencies, and deployment steps for a new genomics analysis applet.
Organize sequencing data
Design upload, metadata, folder, search, and permission workflows for FASTQ, BAM, and VCF files.
Run and monitor analyses
Build a runbook for launching jobs, tracking status, collecting outputs, and handling failures.
Try These Prompts
Plan a first upload
Help me plan how to upload FASTQ files to DNAnexus. Include authentication checks, project selection, folder naming, and metadata fields.
Design an applet checklist
Create a checklist for a DNAnexus applet that takes one BAM file, runs quality control, and returns summary reports.
Build a workflow runbook
Draft a DNAnexus workflow runbook for quality control, alignment, and variant calling across multiple samples.
Review a production pipeline
Review my DNAnexus pipeline plan for production use. Focus on permissions, dependency management, retries, logging, outputs, and cost controls.
Best Practices
- Use placeholder identifiers during planning, then verify every project, file, and applet id before execution.
- Keep credentials out of source code, prompts, shared logs, and generated examples.
- Test DNAnexus apps with small representative datasets before scaling to production workloads.
Avoid
- Do not hardcode API tokens, project secrets, or protected sample identifiers in generated scripts.
- Do not run broad data searches or downloads without checking project scope and permissions.
- Do not deploy applets before confirming dependencies, instance types, output links, and failure behavior.
Frequently Asked Questions
What is DNAnexus Integration for?
It helps users plan and implement DNAnexus apps, data operations, workflow execution, and dxpy automation.
Does it require a DNAnexus account?
Yes. Real uploads, downloads, jobs, and project changes require authenticated DNAnexus access and proper permissions.
Can it run DNAnexus commands automatically?
No. It provides guidance and examples. Users must approve and run commands in their own environment.
Which data types does it cover?
It includes common genomics workflows for FASTQ, BAM, VCF, records, metadata, and analysis outputs.
Can it help with dxpy scripts?
Yes. It documents common dxpy patterns for data objects, jobs, projects, links, and error handling.
How should credentials be handled?
Use approved DNAnexus authentication methods. Do not place real tokens in prompts, generated files, repositories, or logs.
Developer Details
Author
K-Dense-AILicense
Unknown
Skillstore revision
r1
Version notice
The author did not declare a version.
Ref
a25199bc7d6b82598536822d1738eb5d5f54025b
Maintenance freshness
7/18/2026
Usage
5 downloads · 199 views
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