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ngs-bulk-rnaseq

Dispatch bulk RNA-seq requests to FASTQ-to-count QC or count-matrix differential-expression skills using nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor workflows.

63

Quality

79%

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SecuritybySnyk

Low

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tessl review fix ./plugins/ngs-analysis/skills/ngs-bulk-rnaseq/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

82%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 strong, command-dense dispatcher body with excellent actionability and a clearly gated workflow from input confirmation through preflight, test run, real run, and downstream DE. Weaknesses are minor: duplicated local-runner invocation, some harness-internal phrasing, and no explicit post-run output-validation checkpoint.

Suggestions

Collapse the duplicated local-runner invocation: keep the full 'Plugin-Owned Local Paths' command and drop or shorten the partial repeat under 'Local execution run'.

Add an explicit post-run validation checkpoint, e.g., 'Check validation/ and MultiQC summaries in the run envelope before starting differential expression.'

Drop or rewrite the eval-harness sentence in user-facing terms, or move it to a reference doc if it only matters to plugin maintainers.

DimensionReasoningScore

Conciseness

The body is mostly lean: terse input checklists, command blocks, and gating sentences with no concept explanations Claude already knows. Not anchor 5 because the local runner invocation appears twice (full 'Plugin-Owned Local Paths' version and a partial repeat under 'Local execution run'), and 'Do not depend on development-only eval harness paths in a shared package' is harness-internal phrasing that earns little.

4 / 5

Actionability

Commands are fully executable and copy-paste ready for the common cases: the two local runner invocations with explicit flags, four preflight commands, a test-profile kickoff, and a real-run skeleton with concrete parameter values. Placeholders (samplesheet.csv, GRCh38) are appropriately generic.

5 / 5

Workflow Clarity

The sequence is clear and gated: confirm inputs, dispatch, preflight, test kickoff, real run, then DE only after 'biological replicates, design formula, and contrasts' are confirmed, plus strandedness inference before final counts. Not anchor 5 because this batch pipeline lacks an explicit output-validation checkpoint (e.g., inspect MultiQC/validation artifacts before proceeding to DE), keeping a minor validation gap.

4 / 5

Progressive Disclosure

Well-organized single-file skill with clean sections, no nested references, and no inlined bulk that belongs in separate files; the skill exceeds 50 lines, so the simple-skill exception to anchor 5 does not apply. The external script paths ('plugins/ngs-analysis/scripts/...') are not bundled in references/ or scripts/, so they cannot be verified from the skill directory.

4 / 5

Total

17

/

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, tool-rich description with clear niche identity and good natural trigger terms for the bulk RNA-seq domain. Its main weakness is the absence of any explicit 'Use when...' trigger clause, which caps completeness and slightly weakens trigger discoverability.

Suggestions

Add an explicit trigger clause, e.g., 'Use when the user mentions bulk RNA-seq, RNA-seq FASTQ files, read counting, or differential expression analysis.'

Include one or two common user-side synonyms or extensions (e.g., 'DESeq2/edgeR', '.fastq') to broaden natural trigger coverage.

Briefly state what the dispatcher itself does on a request (route vs. execute) to sharpen the 'what' beyond naming tools.

DimensionReasoningScore

Specificity

The description names the domain ('bulk RNA-seq') and concrete capabilities ('FASTQ-to-count QC', 'count-matrix differential-expression') with specific tooling ('nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor'). It stops short of anchor 5 because the only stated action is dispatching/routing rather than several distinct concrete actions, and it does not specify input formats (e.g., FASTQ/BAM) beyond implied ones.

4 / 5

Completeness

The 'what' is clear (dispatch bulk RNA-seq requests to count-QC or DE skills), but there is no 'Use when...' clause or equivalent explicit trigger guidance, which per the judging guidelines caps completeness at 3. Not anchor 4 because the 'when' is not weakly present — it is entirely absent.

3 / 5

Trigger Term Quality

Strong natural domain keywords: 'bulk RNA-seq', 'FASTQ', 'count matrix', 'differential-expression', plus well-known tool names users say ('STAR', 'Salmon', 'MultiQC', 'R/Bioconductor'). Not anchor 5 because common user variations like 'DESeq2', 'gene expression', or file extensions (.fastq, .csv) are absent.

4 / 5

Distinctiveness Conflict Risk

'bulk RNA-seq' is a clear niche with distinct triggers, so it will not fire on unrelated skills. Not anchor 5 because the description covers the same requests as the two child skills it dispatches to ('counts-qc', 'differential-expression'), creating minor overlap risk with those closely related 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-bulk-rnaseq/SKILL.md

Reviewed

Table of Contents

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