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ngs-dna-variant-calling

Dispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.

67

Quality

80%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

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tessl review fix ./plugins/ngs-analysis/skills/ngs-dna-variant-calling/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

82%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.

A highly actionable, well-structured dispatcher body with copy-paste-ready commands and a preflight checkpoint, missing only an explicit post-execution validation loop and with minor trim opportunities.

Suggestions

Add an explicit post-execution validation step (e.g., verify the emitted VCF/callable-loci summary and re-run with adjusted filters if QC fails) to strengthen the feedback loop.

Consider moving the resource-artifact description in the Local Execution Package section into a brief reference or trimming it to the essential flags.

DimensionReasoningScore

Conciseness

It is dense and action-oriented with no padding about basic concepts, but the resource-plan paragraph and a few explanatory sentences could be trimmed.

4 / 5

Actionability

It provides fully executable, copy-paste-ready commands — the preflight script, the parameterized local runner, and two nf-core/sarek skeletons — covering the main cases.

5 / 5

Workflow Clarity

A clear sequence (confirm inputs → dispatch → preflight → execute) with a preflight readiness checkpoint exists, but there is no explicit post-execution verify→fix→retry feedback loop.

4 / 5

Progressive Disclosure

Well-organized sections with clearly signaled one-level references (subtype skills, plugin scripts) and no nested references, though the Local Execution Package section is somewhat dense inline.

4 / 5

Total

17

/

20

Passed

Description

77%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 dispatcher description with strong natural trigger terms and clear distinctiveness, held back only by the lack of an explicit 'Use when...' trigger clause.

Suggestions

Add an explicit 'Use when...' clause naming the trigger scenarios (e.g., 'Use when handling WGS, WES, or targeted DNA variant-calling requests from FASTQ/BAM/CRAM').

Expand the action list slightly (e.g., 'route, plan, and launch') to push specificity toward a comprehensive coverage anchor.

DimensionReasoningScore

Specificity

It lists several concrete actions ('Dispatch WGS, WES, or targeted DNA variant requests', 'plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows') with named tools, but only two verbs keep it just short of comprehensive.

4 / 5

Completeness

The 'what' is clear (dispatch + plan variant workflows) but there is no explicit 'Use when...' clause, so the 'when' is only weakly implied and is capped at 3 per the rubric guideline.

3 / 5

Trigger Term Quality

Natural user terms are comprehensive — WGS, WES, targeted panel, germline, somatic, UMI-panel, plus concrete tool names a bioinformatician would actually say.

5 / 5

Distinctiveness Conflict Risk

It occupies a clear niche as the DNA variant-calling dispatcher routing to distinct germline/somatic/UMI subtypes with named tools, giving 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.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
openai/plugins
Reviewed

Table of Contents

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