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ngs-dna-umi-panel-variants

Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.

60

Quality

76%

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tessl review fix ./plugins/ngs-analysis/skills/ngs-dna-umi-panel-variants/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

75%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.

A lean, expert-oriented body that gets straight to commands, inputs, decision points, and outputs with no filler. The main gaps are the unspecified sample-sheet schema, some duplication between Route and Outputs descriptions, and the absence of an explicit error-recovery path around the preflight/evidence-contract checks.

DimensionReasoningScore

Conciseness

The body is dense and operational with zero concept explanations (fgbio/samtools/bcftools are named without preamble), assuming Claude's competence. Not a 5 because there is redundancy: the postrun-summary and molecular-evidence-contract outputs are described in prose in the Route section and then re-listed in Outputs, which could be merged.

4 / 5

Actionability

Two concrete, copy-paste-ready bash commands with real flags (--umi-mode duplex, --umi-tag RX, --execute) anchor the Route section. Not a 5 because the required input formats are never specified — the sample-sheet TSV columns are unstated and the "lab-validated panel workflow" branch gives no executable path.

4 / 5

Workflow Clarity

The sequence Confirm inputs → Preflight (--emit-install-plan) → Run → Postrun QC review is clear, and the preflight plus the postrun summary ("missing metrics stay explicit in the notes column") act as validation checkpoints. Not a 5 because there is no explicit fix-and-retry loop (e.g. what to do when preflight fails or a sample fails the evidence contract), and decision points are not tied into the step sequence.

4 / 5

Progressive Disclosure

A single-file skill with well-organized, clearly headed sections (Essential Inputs, Route, Decision Points, Outputs) and no monolithic bulk that belongs in a separate file — this matches the simple-skill pattern. Not a 5 because the body references scripts at "plugins/ngs-analysis/scripts/..." that are not present in the bundle, leaving navigation slightly ambiguous about what ships with the skill.

4 / 5

Total

16

/

20

Passed

Description

66%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.

A specific, domain-fluent description that clearly states what the skill does with strong niche vocabulary, but it omits any explicit "when to use this" trigger clause, which both caps completeness and weakens its usefulness for skill selection. Adding a short "Use when..." sentence would resolve the main weakness.

Suggestions

Add an explicit trigger clause, e.g. "Use when processing amplicon or hybrid-capture panel data with UMIs, duplex sequencing, or low-AF (ctDNA/MRD) calling; for panels without molecular barcodes use ngs-dna-germline-variants."

Include a few natural synonyms users actually say — "unique molecular identifiers", "duplex sequencing", "ctDNA", "liquid biopsy", "MRD" — alongside the current technical terms.

State the boundary to adjacent skills in the description itself (ordinary germline panels) so the skill cannot be triggered for the wrong workflow.

DimensionReasoningScore

Specificity

"Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC" names the domain plus several concrete capability areas (duplex consensus, low-frequency calling, target coverage QC). Not a 5 because "run or plan workflows" is really only two actions wrapped around a feature list, leaving minor coverage gaps (no mention of e.g. consensus generation or filtering as distinct actions).

4 / 5

Completeness

The "what" is clear (run/plan UMI-based panel variant workflows), but there is no "Use when..." clause or any equivalent explicit trigger guidance; per the judging guidelines, a missing trigger clause caps completeness at 3. Not a 2 because the "what" half is concrete and specific rather than vague.

3 / 5

Trigger Term Quality

Terms like "UMIs", "duplex consensus reads", "molecular barcodes", "low-frequency calling", and "target coverage" are exactly the natural phrases a genomics user would say. Not a 5 because there are no synonyms or common variations (e.g. "unique molecular identifiers", "UMI-aware", "ctDNA"/"liquid biopsy", "mrDNA"), which the top anchor expects.

4 / 5

Distinctiveness Conflict Risk

The UMI/duplex/low-frequency vocabulary carves out a distinct niche that is unlikely to fire for ordinary germline or general NGS skills. Not a 5 because the description itself does not draw the boundary (e.g. versus plain germline panel calling) — that distinction only appears in the body — so minor overlap risk remains with adjacent DNA-panel skills.

4 / 5

Total

15

/

20

Passed

Validation

100%

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-dna-umi-panel-variants/SKILL.md

Reviewed

Table of Contents

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