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nextflow-development

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

76

Quality

95%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

SKILL.md
Quality
Evals
Security

Quality

Content

92%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 well-structured, highly actionable skill body with a sequenced workflow, explicit validation checkpoints, and clean progressive disclosure to verified reference files. Only minor conciseness trimming is warranted.

Suggestions

Tighten the Disclaimer/Attribution/Licenses sections to a few lines each to reclaim tokens without losing the safety/licensing signal.

Consider collapsing the 'Target users' sentence into the opening paragraph to avoid a separate prose block.

DimensionReasoningScore

Conciseness

The body is largely lean — tables, commands, and checklists with no concept-padding — but the Disclaimer/Attribution/Licenses sections and the target-users sentence could be trimmed slightly. Not a 5 because a few tokens do not strictly earn their place.

4 / 5

Actionability

Provides copy-paste-ready commands for each pipeline (test profile, full run), concrete samplesheet CSV formats, genome management, and resource-limit flags covering the common cases.

5 / 5

Workflow Clarity

A clear Steps 0–6 checklist with explicit 'MUST pass' validation checkpoints, decision points requiring user confirmation, output verification (ls/grep), and feedback loops routing failures to troubleshooting.

5 / 5

Progressive Disclosure

The SKILL.md is an overview pointing to well-signaled, one-level-deep references (geo-sra-acquisition, troubleshooting, installation, pipelines/*), all of which exist as real bundle files; details are appropriately split out.

5 / 5

Total

19

/

20

Passed

Description

100%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 strong, concise description that concretely states capabilities, enumerates natural trigger terms, and explicitly covers both what the skill does and when to use it. It occupies a distinct niche with minimal overlap risk.

DimensionReasoningScore

Specificity

Names the domain (nf-core pipelines) and multiple concrete actions — running rnaseq, sarek, and atacseq on either local FASTQs or public GEO/SRA datasets — with comprehensive coverage of the supported analyses.

5 / 5

Completeness

Explicitly answers both 'what' ('Run nf-core bioinformatics pipelines...') and 'when' ('Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data...') plus a dedicated 'Triggers on...' clause with concrete phrases.

5 / 5

Trigger Term Quality

Comprehensive natural trigger terms including nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, and GSE/GSM/SRR accessions that users would actually say.

5 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (nf-core/Nextflow sequencing pipelines) with distinct triggers like GSE/GSM/SRR accessions, making conflict with unrelated skills minimal.

5 / 5

Total

20

/

20

Passed

Validation

87%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

relative_links

Relative link issues: 6 deeper-than-1-level

Warning

referenced_paths_exist

Referenced path issues: 12 deeper-than-1-level

Warning

Total

14

/

16

Passed

Repository
anthropics/knowledge-work-plugins
Reviewed

Table of Contents

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