ngs-bcl-to-fastq

Validate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.

Quality

83%

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

85%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 well-structured, highly actionable skill body with explicit validation checkpoints and clean sectioning; its only weakness is mild cross-section redundancy that could be tightened.

Suggestions

Consolidate the bcl-convert/no-download boundary into one section and have the Kickoff Pattern reference it rather than restating the command and license caveat.

Consider moving the Metrics Review checklist into a references file to keep SKILL.md as an overview, if the skill grows further.

Dimension	Reasoning	Score
Conciseness	Mostly efficient and free of concept-overexplaining, but the bcl-convert invocation and the 'do not download proprietary software' boundary each recur across the Public Tool Boundary, Local Execution Package, and Kickoff Pattern sections, so it could be tightened.	2 / 3
Actionability	Provides copy-paste-ready executable commands — the preflight script, run_bcl_to_fastq.py with explicit flags, and the direct bcl-convert invocation — with specific placeholder paths rather than pseudocode.	3 / 3
Workflow Clarity	Clear sequenced flow (Preflight → Validation Checklist → confirm-before-execute Kickoff → Metrics Review) with explicit checkpoints and a validation checklist for this batch conversion operation, avoiding the missing-validation cap.	3 / 3
Progressive Disclosure	No bundle files exist and the body has no nested file references; content is cleanly split into well-labeled, navigable sections, which satisfies the well-organized-sections criterion for a self-contained skill.	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, well-scoped third-person description with strong trigger terms and low conflict risk, weakened only by the absence of an explicit 'Use when' trigger clause.

Suggestions

Append an explicit trigger clause, e.g. 'Use when the user has an Illumina BCL run folder, needs to demultiplex a sequencing run, or asks about BCL-to-FASTQ conversion.'

Add common natural variations users might say ('bcl2fastq', 'convert BCL to FASTQ', 'demux a run') to broaden trigger coverage.

Dimension	Reasoning	Score
Specificity	Lists many concrete actions — 'Validate Illumina BCL run folders and sample sheets', 'plan demultiplexing', 'review index/UMI/lane choices', 'run BCL-to-FASTQ conversion', 'interpret demux metrics' — matching the anchor for multiple specific concrete actions.	3 / 3
Completeness	It comprehensively answers 'what' but offers no explicit 'when' trigger: there is no 'Use when...' clause, so per the rubric guideline completeness is capped at 2.	2 / 3
Trigger Term Quality	Natural NGS terms a user would say — 'BCL', 'FASTQ', 'demultiplexing', 'demux', 'Illumina', 'run folder', 'sample sheet' — give strong coverage rather than opaque jargon.	3 / 3
Distinctiveness Conflict Risk	The Illumina BCL-to-FASTQ demultiplexing niche is sharply defined with distinct triggers, making conflict with other skills unlikely.	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-bcl-to-fastq/SKILL.md
Commit: 11c74d6

Reviewed: 17 days ago

Table of Contents

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