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dnanexus-integration

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

Quality

90%

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SKILL.md
Quality
Evals
Security

Quality

Content

100%Weight 40%Scale 1-5

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

An exemplary integration skill body: lean, current-aware (explicit deprecation callouts and a versioned baseline), fully executable guidance with strong safety gates around destructive and billable operations, and a clean one-level-deep reference structure that routes each task to the right file. No material weaknesses found.

DimensionReasoningScore

Conciseness

The body is dense with non-obvious platform facts Claude cannot know (deprecated `systemRequirements` placement, exact-match default of `find_data_objects`, `get_output_ref()` must not be wrapped in `dxlink()`, 50 MB Upload Agent threshold, `DXExecDependencyError`/`AppInsufficientResourceError` policy requirements) and contains no basic-concept padding. Not 4: volatile facts are grouped under 'Current Platform Guidance' with explicit deprecation callouts, and version pins serve reproducible installs, so nothing reads as trimmable over-explanation.

5 / 5

Actionability

Every workflow ships copy-paste-ready commands: `dx upload --path --property`, a complete `dxpy.find_data_objects()` call with all kwargs, `dx run --input-json-file --destination --cost-limit`, `dx find executions --created-after=-2h`, and a full DXApplet chaining example. Not 4: code and commands cover the common cases with real flags and resolved placeholders; no pseudocode anywhere.

5 / 5

Workflow Clarity

Clear sequence (Install → Safe Preflight checklist → routing table → core workflows) with explicit validation checkpoints for destructive/batch operations: resolve names to immutable IDs and check duplicates before mutation, `validate_dxapp.py --strict` before `dx build`, `dx run -h` before launch, confirmation gates before billable/destructive actions, and re-describing remote state before classifying failure. Not 4: validation and error-recovery checkpoints are explicit, so the destructive/batch cap at 3 does not apply and no minor validation gap remains.

5 / 5

Progressive Disclosure

A 'Choose the Right Path' routing table maps each goal to a reference file and preferred interface, an annotated Reference Index lists all nine one-level-deep reference files, and both bundled scripts are invoked with correct relative paths (all verified to exist). Not 4: content is appropriately split between a lean overview and references, with no nested or buried references.

5 / 5

Total

20

/

20

Passed

Description

75%Weight 40%Scale 1-5

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 specific, well-scoped, third-person description with strong platform trigger terms and low conflict risk. Its single material weakness is the absence of any explicit 'when to use' trigger clause, which caps completeness and leaves WDL/CWL workflow-import users without natural entry points.

Suggestions

Add an explicit trigger clause, e.g. 'Use when working with DNAnexus projects, dx CLI commands, dxpy automation, dxapp.json, or importing WDL/CWL/Nextflow pipelines to the platform.'

Include 'WDL' and 'CWL' as trigger terms, since dxCompiler-based WDL/CWL import is a supported capability users would name directly.

Keep the current third-person verb style ('Builds', 'Supports') while adding the trigger clause — it already avoids first/second-person pitfalls.

DimensionReasoningScore

Specificity

Lists multiple concrete, third-person actions — 'Builds and operates reproducible genomics workloads', 'Supports DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation' — covering build, run, operate, and transfer comprehensively. Not 4: no meaningful gap in coverage of the skill's scope; every action names a concrete platform artifact.

5 / 5

Completeness

Has a clear 'what' (builds/operates DNAnexus workloads with named tools) but no 'Use when...' clause or equivalent explicit trigger guidance, capping completeness at 3 per the judging guidelines. Not 4: the 'when' is not even weakly implied anywhere in the description.

3 / 5

Trigger Term Quality

Good natural keyword coverage: 'DNAnexus', 'dx CLI', 'dxpy', 'apps/applets', 'native workflows', 'dxCompiler', 'Nextflow', 'dxapp.json'. Not 5: misses natural variations users would say, notably 'WDL' and 'CWL' (supported via dxCompiler per the body) and generic phrases like 'upload files to DNAnexus'. Not 3: coverage clearly exceeds 'some relevant keywords'.

4 / 5

Distinctiveness Conflict Risk

Clear niche: every trigger is anchored to the DNAnexus platform ('DNAnexus', 'dx CLI', 'dxpy', 'dxapp.json', 'applets'), which is unambiguous and distinct from adjacent bioinformatics pipeline skills. Not 4: the only overlap (generic 'Nextflow'/'workflow' terms) is fully scoped by 'on DNAnexus', leaving minimal conflict risk.

5 / 5

Total

17

/

20

Passed

Validation

100%

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

Reviewed

Table of Contents

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