nf-core-reviewer

nf-core-reviewer is an agent for Claude Code from jonasscheid/claude-nfcore-plugin. It costs 40 tokens per session (649 once invoked), scanned A, original, MIT.

A code reviewer for nf-core projects, which are shared bioinformatics workflows built with Nextflow. It checks workflow code, module structure, tests, naming and configuration against nf-core rules.

In plain words
What is it for?
Use it to review pull requests, inspect Nextflow pipeline changes and check whether modules, containers, tests and outputs follow nf-core practices.
Why use it?
It finds standards and quality problems before code is merged, making reviews more consistent.

Agent for Claude Code

Written for Claude Code: disable-model-invocation in frontmatter. Also seen: model in frontmatter.

Runs only inside its plugin — its command needs a path that Claude Code sets for a plugin’s own hooks and for nothing else. Install the plugin, not this.

Part of the nf-core plugin — 4 skills, 6 agents, 2 hooks shipped together

Good fit Use it to review pull requests, inspect Nextflow pipeline changes and check whether modules, containers, tests and outputs follow nf-core practices.

Compare 6 agents from other repositories ↓
Install

Getting it into your agent

This one installs as part of its plugin. Adding the marketplace and installing the plugin brings it with everything else the plugin ships.

Claude Code
/plugin marketplace add jonasscheid/claude-nfcore-plugin
Claude Code
/plugin install nf-core

Made for: Claude Code.

Or install nf-core, the plugin that ships this one along with the rest of its 4 skills, 6 agents, 2 hooks.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for nf-core-reviewer

README.md
[![agentmods](https://agentmods.dev/badge/agents/jonasscheid/claude-nfcore-plugin/nf-core-reviewer.svg)](https://agentmods.dev/agents/jonasscheid/claude-nfcore-plugin/nf-core-reviewer)
Your own site
<a href="https://agentmods.dev/agents/jonasscheid/claude-nfcore-plugin/nf-core-reviewer"><img src="https://agentmods.dev/badge/agents/jonasscheid/claude-nfcore-plugin/nf-core-reviewer.svg" alt="Measured on agentmods" height="20"></a>
Per session 40 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 649 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00040 $0.00649
Opus 5 $0.00020 $0.00324
Sonnet 5 $0.00008 $0.00130
Haiku 4.5 $0.00004 $0.00065

Measured 8d ago against content hash fa67009e2e0f, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

nf-core-reviewer scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

agents/nf-core-reviewer.md · 91 lines

How it starts

The opening of the file, as written. The whole thing — 91 lines — stays where its author put it; the contents beside it link to each section on GitHub.

nf-core Code Reviewer

You are an nf-core code reviewer. Your role is to review Nextflow code for compliance with nf-core standards and best practices, providing constructive feedback.

Read ${CLAUDE_PLUGIN_ROOT}/shared/conventions.md for nf-core conventions, strict syntax rules, and naming standards.

Review Checklist

1. Nextflow Conventions

  • Uses lowercase channel. not Channel.
  • Channel names prefixed with ch_
  • No strict syntax violations (for/while/switch/imports)
  • Explicit closure parameters (not it)

2. Process Definitions

  • Tag: tag "$meta.id"
  • Appropriate resource label
  • Container defined correctly (no :latest)
  • when block for conditional execution
  • versions.yml output
  • stub block for testing
  • Output patterns: path("${prefix}.ext") not path("*.ext")

3. Parameter & Channel Naming

  • snake_case parameters
  • Boolean params use negative form (skip_X)
  • Documented in nextflow_schema.json

4. Module Structure

  • Follows nf-core module template
  • main.nf, meta.yml present
  • Tests exist (main.nf.test)

5. Code Quality

  • Clear variable names, logical flow
  • DRY, modular design
  • Validates inputs where appropriate

6. Testing

  • Tests for all major code paths
  • Meaningful assertions
  • Snapshots for outputs

Review Output Format

Organize feedback by priority:

Critical Issues (Must Fix)

  • Breaking changes, missing required elements, incorrect functionality

Warnings (Should Fix)

  • Style violations, missing documentation, suboptimal patterns

Suggestions (Consider)

  • Improvements, optimizations, code clarity

Review Process

  1. Understand Context: What is the PR trying to achieve?
  2. Check Structure: File organization, naming conventions
  3. Review Logic: Process definitions, channel operations
  4. Verify Tests: Coverage and quality
  5. Provide Feedback: Constructive, specific, actionable

Read the full file on GitHub · 91 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 8d ago First seen · 91 lines · 40 tokens per session scan A fa67009e2e0f

Subscribe to this mod's changes

nf-core-reviewer is an agent published in the GitHub repository jonasscheid/claude-nfcore-plugin (10 stars, last pushed 3mo ago), licensed MIT. It adds 40 tokens to every session and 649 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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