nextflow

Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows, container and executor configuration, HPC/SLURM or cloud deployment, and failed or resumed pipeline runs.

Quality

94%

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Securityby

Low

Low-risk findings worth noting

Quality

Content

86%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, well-structured body: fully executable commands and examples with explicit verification steps, and excellent progressive disclosure across seven real one-level-deep reference files. The only notable weakness is modest verbosity in the conceptual Overview section and error-recovery detail deferred to references.

Suggestions

Tighten the Overview section: drop or compress background Claude already knows (what Nextflow is, 'dominant in bioinformatics', dataflow programming basics) and keep only version-specific and skill-orienting facts.

Add one inline feedback loop for the most common failure mode (e.g., a two-line 'if tasks re-run unexpectedly, check cache invalidation — see references/configuration.md' step in the Quick Start) so error recovery is visible without opening a reference.

Trim rhetorical phrasing such as 'it changes everything' in the Two Modes of Work intro; a plain statement of the routing rule is more token-efficient.

Dimension	Reasoning	Score
Conciseness	The body is dominated by dense, high-value tables (CLI references, routing table) and tight bullet lists, but the Overview spends several sentences on background Claude largely knows ("Nextflow is a workflow language and runtime for building reproducible, portable, scalable data pipelines. It is dominant in bioinformatics...") and includes a few rhetorical flourishes ("it changes everything") that could be trimmed.	4 / 5
Actionability	Fully executable, copy-paste-ready guidance throughout: pinned install commands with verification steps, a real run command with samplesheet inputs, a complete minimal pipeline that the text states was actually executed with Nextflow 26.04.6, and concrete CLI tables covering the common cases.	5 / 5
Workflow Clarity	The "Two Modes of Work" routing table plus sequenced Quick Start (verify java → install → smoke test on the release's test profile → real pinned run) gives a clear path with explicit validation checkpoints ("nextflow info # verify", check sample identity and outputs independently of exit status). It falls just short of the top anchor because detailed error-recovery/feedback loops (e.g., cache debugging) are delegated to reference files rather than stated inline.	4 / 5
Progressive Disclosure	The body is a well-organized overview (~200 lines) that routes by goal to seven real, self-contained reference files; the Reference Files section describes each one clearly, and the references are one level deep (sibling cross-links only, no nested see-details chains), matching the top anchor.	5 / 5
	Total	18 / 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.

An exemplary description: third-person, concrete actions, explicit 'Use for' triggers including file extensions and synonyms, and a clearly distinct niche. Every dimension sits at the top anchor without padding or over-claiming.

Dimension	Reasoning	Score
Specificity	The description lists multiple specific concrete actions — "Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows" — comprehensively covering the skill's scope in third-person voice, matching the top anchor.	5 / 5
Completeness	It explicitly answers both questions: a clear "what" ("Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows") followed by an explicit "Use for..." clause with concrete trigger phrases, mirroring the top anchor example.	5 / 5
Trigger Term Quality	Comprehensive natural-term coverage including file extensions and synonyms: "Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows, container and executor configuration, HPC/SLURM or cloud deployment, and failed or resumed pipeline runs" — terms a user would naturally say.	5 / 5
Distinctiveness Conflict Risk	The Nextflow/nf-core niche is unambiguous with distinct triggers (.nf, nextflow.config, nf-test, SLURM); there is minimal risk of this firing for an unrelated skill.	5 / 5
	Total	20 / 20 Passed

Validation

100%

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 — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: K-Dense-AI/scientific-agent-skills
Path: skills/nextflow/SKILL.md
Commit: 1549884

Reviewed: 4 days ago

Table of Contents

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