dnanexus-integration

Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.

Quality

92%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

85%

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-architected skill body with executable guidance, strong destructive-operation checkpoints, and clean one-level-deep progressive disclosure. Its only weakness is inline version/date baseline detail that the rubric expects to live in a centralized or deprecated section rather than the main overview.

Suggestions

Move the version baseline (dxpy==0.410.0, dxCompiler 2.17.0, 2026-07-23 verification date) into references/sources.md and keep only a short pointer in the body, so time-sensitive detail does not bloat the overview.

Consider condensing the 'Current Platform Guidance' bullet list into the relevant reference files (configuration.md, job-execution.md) and retaining only the most load-bearing rules inline.

Centralize deprecated-pattern notes (e.g. top-level `resources` / `runSpec.systemRequirements`) in a single 'Deprecated' subsection of configuration.md rather than stating them inline.

Dimension	Reasoning	Score
Conciseness	The body is lean and assumes Claude's competence with no concept-explanation padding, but it carries inline time-sensitive specifics (dxpy==0.410.0, dxCompiler 2.17.0, a 2026-07-23 baseline date) and a broad 'Current Platform Guidance' list rather than centralizing that detail in a deprecated/baseline section, which the rubric says should penalize conciseness.	2 / 3
Actionability	It provides fully executable, copy-paste-ready commands and code — pinned installs, `dx run` with `--input-json-file --destination --cost-limit`, a complete dxpy `find_data_objects` call with real kwargs, and scripted validator invocations with flags.	3 / 3
Workflow Clarity	Risky batch/destructive operations are sequenced with explicit checkpoints: a read-only Safe Preflight, an Operating Contract requiring confirmation before billable/destructive actions, 'show resolved IDs and impact before destructive operations', and feedback loops (re-describe remote state before classifying failure; treat malicious-file warnings as a stop condition).	3 / 3
Progressive Disclosure	SKILL.md is a clear overview with a 'Choose the Right Path' routing table and a Reference Index pointing one level deep to nine real reference files plus two bundled scripts, all verified to exist and clearly signaled, with detail appropriately split out of the main file.	3 / 3
	Total	11 / 12 Passed

Description

100%

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A tight, third-person description that concretely states capabilities and tools while giving an explicit 'Use for' trigger clause. It is specific, complete, and distinct with no vague fluff or over-claims.

Dimension	Reasoning	Score
Specificity	The description lists multiple concrete actions (build/operate workloads, data transfers, dxapp.json development, execution monitoring, workflow import, project automation) alongside named tools (dx CLI, dxpy, apps/applets, dxCompiler, Nextflow), matching the 'lists multiple specific concrete actions' anchor.	3 / 3
Completeness	It explicitly answers both 'what' (build and operate reproducible genomics workloads with listed tools) and 'when' via an explicit 'Use for ...' trigger clause, satisfying the top anchor.	3 / 3
Trigger Term Quality	It uses natural terms a DNAnexus user would say — 'DNAnexus', 'dx CLI', 'dxpy', 'apps/applets', 'workflows', 'dxCompiler', 'Nextflow', 'data transfers', 'execution monitoring' — giving good coverage rather than opaque jargon.	3 / 3
Distinctiveness Conflict Risk	The DNAnexus platform niche with named genomics tooling is clearly distinct and unlikely to trigger for unrelated skills.	3 / 3
	Total	12 / 12 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: K-Dense-AI/scientific-agent-skills
Path: skills/dnanexus-integration/SKILL.md
Commit: 757b63b

Reviewed: about 11 hours ago

Table of Contents

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