Getting it into your agent
There is no command for this one: it runs only inside a plugin, and the catalogue could not identify which plugin ships it. The source is linked below.
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.
[](https://agentmods.dev/instructions/nextflow-io/agent-skills/claude-md)<a href="https://agentmods.dev/instructions/nextflow-io/agent-skills/claude-md"><img src="https://agentmods.dev/badge/instructions/nextflow-io/agent-skills/claude-md.svg" alt="Measured on agentmods" height="20"></a>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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.01001 | $0.01001 |
| Opus 5 | $0.00500 | $0.00500 |
| Sonnet 5 | $0.00200 | $0.00200 |
| Haiku 4.5 | $0.00100 | $0.00100 |
Grade A, and why
agent-skills CLAUDE.md 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 6d 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.
How it starts
The opening of the file, as written. The whole thing — 50 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
What this repo is
A Claude Code plugin that bundles agent skills for building and running Nextflow pipelines with modules from the Nextflow Registry. There is no application code, build step, or test suite — the deliverable is the set of SKILL.md files, each a Markdown document with YAML frontmatter that instructs an agent how to perform a task.
Skills follow the Agent Skills specification so they work in any compatible agent (Claude Code, Codex, Cursor, OpenCode).
Layout
.claude/commands/— repo-local dev tooling, not shipped to plugin users.eval.md(/eval <migration> <github-url> [branch]) exercises amigrate-nextflow-codemigration against a real pipeline and reports where the skill's instructions fall short..claude-plugin/plugin.json— plugin manifest (name, version, keywords). Bumpversionwhen releasing.scripts/nextflow-typecheck.sh— drives the Nextflow language server headlessly and prints diagnostics for a project. This is how skills check for type errors;nextflow lintonly checks syntax.skills/<name>/SKILL.md— one skill per directory; the directory name must match thename:in frontmatter.- Skills may bundle resources:
references/*.md(loaded on demand). Shared executable helpers live in the top-levelscripts/(e.g.scripts/nextflow-language-server.sh), referenced from skills via${CLAUDE_PLUGIN_ROOT}/scripts/.... .mcp.json— declares the Seqera MCP server, which allows the agent to interact with Seqera Platform.
The skills and how they relate
install-nextflow— installs/upgrades Nextflow and the Java 17+ prerequisite (via SDKMAN). Other skills require Nextflow 26.04+.run-module— runs a single Registry module vianextflow module search/view/run. Self-contained (no MCP).create-workflow— composes multiple modules into a pipeline. Delegates torun-module(via theSkilltool) to validate each module before composing.launch-workflow— launches pipelines on Seqera Platform for cloud/HPC execution. Requires the seqera MCP (mcp__seqera__*tools) — declared inallowed-tools.migrate-nextflow-code— migrates pipeline code to newer language features.
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.
- 6d ago First seen · 50 lines · 1,001 tokens per session scan A 0f2e4952674e
agent-skills CLAUDE.md is an instructions file published in the GitHub repository nextflow-io/agent-skills (21 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 1,001 tokens to every session, about $0.0050 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 2026-08-30.
Other instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.