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ngs-shotgun-metagenomics

Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.

64

Quality

76%

Does it follow best practices?

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SecuritybySnyk

Passed

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tessl review fix ./plugins/ngs-analysis/skills/ngs-shotgun-metagenomics/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.

The body is concise, highly actionable, and well-structured with executable commands and a clear workflow sequence including preflight validation. It is self-contained with no bundle references, organized into clearly navigable sections.

DimensionReasoningScore

Conciseness

The body is action-oriented with no concept lectures Claude already knows; every section earns its place, with only minor phrasing that could be tightened.

4 / 5

Actionability

Provides fully executable, copy-paste-ready commands (preflight, run_fastq_assay_package.py, run_shotgun_metagenomics.py with concrete flags, a kraken2 skeleton, nextflow run) covering the common cases.

5 / 5

Workflow Clarity

Sequences preflight -> local QC package -> backend profiling with a validation checkpoint (ngs_preflight.py --emit-install-plan), --execute gating, and a guardrails section; minor validation gaps keep it just below the explicit feedback-loop anchor.

4 / 5

Progressive Disclosure

No bundle files exist, so the body is a self-contained, well-sectioned SKILL.md with clear navigation (Essential Inputs, Preflight, Local Execution Package, Kickoff Pattern, Visualization Outputs, Guardrails); length slightly exceeds the under-50-line simple-skill threshold, keeping it just below 5.

4 / 5

Total

17

/

20

Passed

Description

70%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 distinctive, naming concrete capabilities and a clear toolset for shotgun metagenomics. Its main weakness is the absence of an explicit 'Use when...' trigger clause, which caps completeness.

Suggestions

Add an explicit 'Use when...' clause naming natural trigger phrases, e.g. 'Use when processing shotgun metagenomic FASTQs for taxonomic or functional profiling.'

Include common user synonyms like 'FASTQ' or 'reads' to broaden trigger-term coverage.

Keep the named tool list but ensure the trigger guidance surfaces before the tool enumeration so activation intent is unambiguous.

DimensionReasoningScore

Specificity

Names concrete capabilities ("QC, host-depletion, taxonomic profiling, and functional profiling") and specific tools ("nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN"), with only minor coverage gaps versus the comprehensive anchor.

4 / 5

Completeness

Provides a clear "what" but has no "Use when..." clause or equivalent explicit trigger guidance, which caps completeness at 3 per the rubric guideline.

3 / 5

Trigger Term Quality

Includes natural terms users would say ("shotgun metagenomics", "QC", "host-depletion", "taxonomic profiling", "functional profiling") but omits common synonyms like "FASTQ" or "reads", leaving a few natural phrases missing.

4 / 5

Distinctiveness Conflict Risk

Carves a clear niche (shotgun metagenomics with named profiling tools) distinct from other NGS skills, with minimal risk of triggering for the wrong skill.

5 / 5

Total

16

/

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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