claw-amplicon-qc

16S/18S rRNA amplicon preprocessing — from raw paired-end FASTQ files through N removal and primer trimming, producing outputs ready for DADA2 quality filtering and denoising. Deliberately stops before quality-filtering decisions that require researcher judgment.

Quality

73%

Does it follow best practices?

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Securityby

Passed

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tessl review fix ./skills/claw-amplicon-qc/SKILL.md

Quality

Content

77%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 highly actionable with a well-sequenced, validated workflow and concrete commands, but it carries redundancy that hurts conciseness and keeps everything in a single large file with no progressive disclosure. Splitting reference material and tightening repeated sections would lift the weaker dimensions.

Suggestions

De-duplicate the threshold list (keep it only in the CLI Reference table) and consolidate flag descriptions to remove Gotchas/Algorithm overlap.

Move the full captured example output and/or the Algorithm/Methodology rationale into a references/ file referenced one level deep from SKILL.md to improve progressive disclosure.

Trim or repurpose the 'Why This Exists' section into a brief scope statement to reduce editorial padding.

Dimension	Reasoning	Score
Conciseness	Mostly efficient domain guidance, but thresholds are listed twice (CLI table and Algorithm 'Key thresholds'), flags are restated in Gotchas, and the editorial 'Why This Exists' section pads the document with content that could be trimmed.	3 / 5
Actionability	Copy-paste-ready Rscript invocations, full required/optional argument tables with defaults, concrete primer sequences, and a captured example output fully cover the common cases.	5 / 5
Workflow Clarity	A clearly sequenced Discover→Pre-flight→Stage 1-5→Report pipeline with explicit validation checkpoints (preflight abort, 1% retention backstop, fail-loud) and feedback loops for the batch operation.	5 / 5
Progressive Disclosure	Good section headers structure the content, but it is a ~340-line monolithic file with the full example output, methodology, and citations inlined and no bundle references to deeper material — content that could be split stays inline.	3 / 5
	Total	16 / 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 well-scoped with strong domain keywords and a clear boundary, but it lacks an explicit 'Use when...' trigger clause, which limits completeness. It is highly distinctive within a bioinformatics skill ecosystem.

Suggestions

Append an explicit trigger clause, e.g. 'Use when preprocessing 16S/18S paired-end FASTQ files before DADA2 denoising.'

Mention common file extensions (.fastq.gz) and terms like 'microbiome QC' to broaden natural trigger coverage.

Dimension	Reasoning	Score
Specificity	Names concrete actions — 'raw paired-end FASTQ files through N removal and primer trimming, producing outputs ready for DADA2' — several specific capabilities with minor gaps (no mention of seqkit stats or preflight orientation check).	4 / 5
Completeness	Clearly states what the skill does, but offers no explicit 'Use when...' trigger clause — the 'when' is only weakly implied, capping completeness at 3 per the rubric guideline.	3 / 5
Trigger Term Quality	Strong natural keyword coverage ('16S/18S', 'amplicon', 'FASTQ', 'DADA2', 'primer trimming', 'N removal') a user would actually say, though file extensions and 'microbiome' variants are absent.	4 / 5
Distinctiveness Conflict Risk	A clear niche (16S/18S preprocessing that deliberately stops before DADA2 quality-filtering) with distinct triggers and an explicit boundary against the downstream DADA2 skill, giving minimal conflict risk.	5 / 5
	Total	16 / 20 Passed

Validation

93%

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 — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_field	'metadata' should map string keys to string values	Warning

	Total	15 / 16 Passed

Repository: ClawBio/ClawBio
Path: skills/claw-amplicon-qc/SKILL.md
Commit: d30153a

Reviewed: 3 days ago

Table of Contents

Discovery Implementation Validation

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