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dnanexus-integration

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.

59

Quality

70%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

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tessl review fix ./scientific-skills/Data Analysis/dnanexus-integration/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

65%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.

The body is well-structured with executable examples and excellent progressive disclosure to real reference files. It is held back by generic boilerplate padding and missing validation checkpoints in its batch/destructive workflows.

Suggestions

Trim the generic 'When to Use', 'Key Features', and 'Implementation Details' boilerplate that duplicates the description and adds little DNAnexus-specific signal.

Add explicit validation/verification checkpoints to batch and multi-step pipeline workflows (e.g., verify job state before downloading outputs, validate FASTQ/BAM before downstream steps).

Replace the 'See ## Overview above for related details' cross-reference with concrete inline guidance to avoid navigational ambiguity.

DimensionReasoningScore

Conciseness

The core capability and code sections are efficient, but generic boilerplate ('When to Use' bullets, 'Key Features', 'Implementation Details' with 'See ## Overview above') pads the document with content that could be trimmed.

3 / 5

Actionability

Provides multiple concrete, executable code blocks (upload/analyze, search, app creation, batch, multi-step pipeline) and commands like 'dx login' and 'uv pip install dxpy', with only minor gaps such as the placeholder 'quality_filter' tool.

4 / 5

Workflow Clarity

A sequenced decision tree and common patterns are present, but batch and data-organization operations lack validation/verification checkpoints, so workflow clarity is capped at 3 per the batch/destructive-operation guideline.

3 / 5

Progressive Disclosure

A clear overview routes each of five capability areas to one-level-deep reference files (all verified present: app-development.md, data-operations.md, job-execution.md, python-sdk.md, configuration.md), with bulk detail appropriately split out.

5 / 5

Total

15

/

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.

The description is specific and distinct, listing concrete DNAnexus actions with relevant file-format triggers. Its main weakness is the absence of an explicit 'Use when...' clause, leaving the trigger condition only weakly implied.

Suggestions

Add an explicit 'Use when...' trigger clause, e.g. 'Use when working with DNAnexus, building genomics apps/applets, or processing FASTQ/BAM/VCF data.'

Include a few natural synonyms users would say — sequencing data, bioinformatics, alignment, variant calling — to broaden trigger coverage.

Consider adding dotted file extensions (.fastq, .bam, .vcf) alongside the existing FASTQ/BAM/VCF tokens.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF' — giving comprehensive coverage of the platform's capabilities.

5 / 5

Completeness

The 'what' is clearly stated, but the 'when' is only a weak purpose clause ('for developing and executing genomics pipelines') with no explicit 'Use when...' trigger guidance, which caps completeness at 3.

3 / 5

Trigger Term Quality

Includes strong natural keywords (DNAnexus, apps/applets, FASTQ/BAM/VCF, dxpy, genomics pipelines) with file extensions, but misses common synonyms like sequencing, bioinformatics, alignment, or variant calling.

4 / 5

Distinctiveness Conflict Risk

'DNAnexus cloud genomics platform' names a clear niche with distinct triggers and minimal risk of firing for an unrelated skill.

5 / 5

Total

17

/

20

Passed

Validation

87%

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

Validation14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

referenced_paths_exist

Referenced path issues: 2 missing

Warning

Total

14

/

16

Passed

Repository
aipoch/medical-research-skills
Reviewed

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