ngs-epigenomics-peaks

Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.

Quality

85%

Does it follow best practices?

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Adds up to 20 points to the overall score

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Securityby

Low

Low-risk findings worth noting

Quality

Content

87%Weight 40%Scale 1-3

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

A concise, highly actionable dispatcher body with clean section structure and a clear handoff to deeper skills, weakened only by the absence of explicit validation checkpoints before proceeding to real analysis.

Suggestions

Add an explicit checkpoint after preflight/readiness (e.g. 'Only proceed to alignment when peak_calling_readiness.json reports all checks passing; otherwise fix sample-sheet paths and re-run').

Frame the readiness JSON as a validation gate with a fix-and-retry loop to support the batch nature of these workflows.

Dimension	Reasoning	Score
Conciseness	The body is lean, assumes Claude knows what nf-core and these assays are, and uses commands and tight lists rather than concept explanations; not 2 because no padded or unnecessary explanation is present.	3 / 3
Actionability	Provides concrete, copy-paste-ready commands (preflight script, run_fastq_assay_package.py with flags, nextflow run invocations) with specific arguments; not 2 because the code is executable rather than pseudocode.	3 / 3
Workflow Clarity	Steps are sequenced via sections (confirm inputs, choose workflow, preflight, execute) and a readiness JSON is produced, but there is no explicit validate->fix->retry checkpoint gating progression, which the guidelines cap at 2 for batch operations; not 3 because checkpoints are implicit, not 1 because the sequence is clearly present.	2 / 3
Progressive Disclosure	Content is split into well-organized sections with a clear handoff to named assay-specific deep skills (one level deep), no bundle files exist to misorganize, and there is no monolithic wall; not 2 because structure and navigation are clear.	3 / 3
	Total	11 / 12 Passed

Description

82%Weight 40%Scale 1-3

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, third-person description with strong natural trigger terms and low conflict risk, but it lacks an explicit 'Use when...' trigger clause, capping completeness at 2.

Suggestions

Add an explicit trigger clause such as 'Use when the user has ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag data and needs peak-centric analysis.'

Optionally name common user phrasings (e.g. 'peak calling', 'accessibility', 'histone mark') to broaden natural trigger coverage.

Dimension	Reasoning	Score
Specificity	Names four concrete assay types (ATAC-seq, ChIP-seq, CUT&RUN, CUT&Tag) and dispatches them to six named workflow stages (QC, alignment, signal-track, peak-calling, consensus, differential peaks), matching the 'lists multiple specific concrete actions' anchor.	3 / 3
Completeness	It clearly states what the skill does (dispatch to assay-specific workflows) but provides no 'Use when...' clause or equivalent explicit trigger guidance, which the guidelines cap at 2; not 3 because the 'when' is only implied, and not 1 because the 'what' is explicit.	2 / 3
Trigger Term Quality	The assay names plus 'peaks' and 'QC' are exactly the natural terms a genomics user would say when requesting this work; not score 2 because no common variations are missing for this domain.	3 / 3
Distinctiveness Conflict Risk	The highly specific epigenomic assay names define a clear niche unlikely to trigger for unrelated skills; not 2 because the triggers are distinctive rather than broadly overlapping.	3 / 3
	Total	11 / 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: openai/plugins
Path: plugins/ngs-analysis/skills/ngs-epigenomics-peaks/SKILL.md
Commit: 11c74d6

Reviewed: 17 days ago

Table of Contents

Discovery Implementation Validation

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