ngs-atacseq-peaks-qc

Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.

Quality

80%

Does it follow best practices?

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Adds up to 20 points to the overall score

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Securityby

Passed

No findings from the security scan

Quality

Content

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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 explicit QC gating; the main gap is the absence of a rigorous validate→fix→retry feedback loop for a batch bioinformatics workflow.

Dimension	Reasoning	Score
Conciseness	Lean and efficient with no padding and no over-explanation of ATAC-seq concepts; every line — inputs, routing commands, QC gates, outputs — earns its place.	5 / 5
Actionability	Multiple copy-paste-ready command blocks with concrete flags (--bowtie2-index, --blacklist-bed, --tss-bed, --execute) and explicit routing rules between nf-core, the shared package, and the dedicated ATAC runner.	5 / 5
Workflow Clarity	Clear preflight→route→runner sequence with explicit QC gates ('Review before biological interpretation', 'Do not proceed to differential accessibility if…'), but it lacks a strict validate→fix→retry feedback loop.	4 / 5
Progressive Disclosure	Well-organized into clearly labeled sections with no nested references and no bundle files needed, though some inline output specifications could potentially live in a separate reference file.	4 / 5
	Total	18 / 20 Passed

Description

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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 trigger-rich with strong domain action coverage, but it omits an explicit 'Use when…' clause, leaving the 'when' guidance only implied and capping completeness.

Suggestions

Append an explicit trigger clause, e.g. 'Use when the user needs ATAC-seq accessibility analysis from FASTQ or BAM, including QC, peak calling, or differential accessibility.'

Add common phrasings/synonyms a user might say, such as 'open chromatin' or 'accessibility profiling', to broaden trigger coverage.

Briefly state the contrast with antibody-targeted assays (e.g. ChIP-seq/CUT&RUN) in the description itself rather than only in the body, sharpening distinctiveness.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility' — with comprehensive domain coverage.	5 / 5
Completeness	Clear 'what' via the enumerated analyses, but there is no explicit 'Use when…' trigger clause, which caps completeness at 3 per the guidelines.	3 / 5
Trigger Term Quality	Strong natural keywords users say ('ATAC-seq QC', 'TSS enrichment', 'peak-calling', 'differential accessibility') with synonyms, but no file extensions or a couple of common phrasings are missing.	4 / 5
Distinctiveness Conflict Risk	Clearly an ATAC-seq niche with distinct triggers and minimal conflict risk, though slight overlap remains with general NGS/epigenomics skills.	4 / 5
	Total	16 / 20 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-atacseq-peaks-qc/SKILL.md
Commit: 1dc1958

Reviewed: 5 days ago

Table of Contents

Discovery Implementation Validation

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