Name: bioqc-mcp
Rating: 58.4 (1 reviews)
Author: ClawBio

bioqc-mcp

Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation. Exposes an MCP stdio server for live AI integration alongside a ClawBio CLI runner.

Quality

67%

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Securityby

Passed

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tessl review fix ./skills/bioqc-mcp/SKILL.md

Quality

Content

76%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 executable commands and concrete expected outputs, and is well-organized, but its batch QC workflow lacks an explicit output-validation/feedback loop, which caps workflow clarity, and some sections could be offloaded to reference files for tighter progressive disclosure.

Suggestions

Add an explicit validation/feedback step to the workflow (e.g. verify FastQC produced expected outputs per sample; on failure, re-run or report which sample failed) to lift the batch-operation cap on workflow clarity.

Move the Algorithm/Methodology and Citations sections into a separate reference file (e.g. METHODOLOGY.md) referenced one level deep, keeping SKILL.md a lean overview.

Trim the 'Why This Exists' framing to the essential contrast so every remaining token earns its place.

Dimension	Reasoning	Score
Conciseness	The body is mostly efficient with concrete commands and minimal concept explanation, but sections like 'Why This Exists' and 'Integration with Bio Orchestrator' carry a little extra framing that could be trimmed, fitting the 'efficient; minor instances of over-explanation' anchor rather than the lean 5.	4 / 5
Actionability	Provides copy-paste ready CLI commands covering the common cases (full pipeline, MCP mode, chart mode, demo), plus a concrete expected output tree and a report.md excerpt, matching the 'fully executable; copy-paste ready; covers common cases' anchor.	5 / 5
Workflow Clarity	The 7-step workflow is clearly sequenced and opens with a Verify step, but it is a batch operation over all FASTQ files with no output validation or fix-and-retry feedback loop; per the rubric cap, a batch skill missing validation cannot score above 3, so it stays at 3 rather than the 4 'clear sequence with most checkpoints'.	3 / 5
Progressive Disclosure	The skill is a single well-organized file with clear section headers and no nested references (no bundle files exist to defer to), but content such as Algorithm/Methodology and Citations is inlined where a separate reference file could keep the overview leaner, placing it at the 'good structure; minor organization gaps' anchor rather than a fully split 5.	4 / 5
	Total	16 / 20 Passed

Description

58%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 clearly states concrete capabilities across QC and visualization with a dual CLI/MCP interface, but it lacks an explicit 'Use when...' trigger clause and is missing natural user phrases and FASTQ file extensions, capping completeness and trigger-term quality.

Suggestions

Add an explicit 'Use when...' clause naming concrete trigger phrases (e.g. FASTQ quality control, QC reports, per-base quality plots).

Include natural terms and file extensions users would actually say — 'FASTQ files', '.fastq', '.fq.gz', 'QC report' — to improve trigger-term coverage.

Tighten distinctiveness by clarifying what separates this from a plain multiqc-reporter skill (custom chart generation, MCP server).

Dimension	Reasoning	Score
Specificity	Lists several concrete capabilities — 'wrapping FastQC, MultiQC, and custom chart generation', 'Exposes an MCP stdio server', 'ClawBio CLI runner' — with only minor coverage gaps (e.g. specific chart types are not enumerated here), matching the 'several specific actions; minor gaps' anchor rather than the comprehensive 5.	4 / 5
Completeness	It has a clear 'what' but no 'Use when...' clause or equivalent explicit trigger guidance; per the judging guidelines a missing trigger clause caps completeness at 3, so it does not reach the 4 anchor that requires both what and when.	3 / 5
Trigger Term Quality	Contains relevant domain keywords ('sequencing quality control', 'FastQC', 'MultiQC', 'MCP') but omits common natural variations and file extensions users would say (e.g. 'FASTQ', '.fastq', 'QC report'), fitting the 'some relevant keywords but missing common variations' anchor.	3 / 5
Distinctiveness Conflict Risk	The FastQC/MultiQC/MCP niche is mostly distinct with only minor overlap risk against closely related skills (e.g. a plain multiqc-reporter), placing it at the 'mostly distinct; minor overlap risk' anchor rather than the fully-conflict-free 5.	4 / 5
	Total	14 / 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/bioqc-mcp/SKILL.md
Commit: d30153a

Reviewed: 3 days ago

Table of Contents

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