Borrowing it
Nothing to install: this file belongs to nextflow-io/agent-skills. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/nextflow-io/agent-skills/master/AGENTS.mdgit clone --depth 1 https://github.com/nextflow-io/agent-skillsWrote 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/agents-md)<a href="https://agentmods.dev/instructions/nextflow-io/agent-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/nextflow-io/agent-skills/agents-md/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/instructions/nextflow-io/agent-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/nextflow-io/agent-skills/agents-md.svg" alt="Reviewed on agentmods" width="80" 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 | $0.01045 | $0.01045 |
| Opus 5.5 | $0.00418 | $0.00418 |
| Sonnet 5.5 | $0.00209 | $0.00209 |
| Haiku 4.5 | $0.00104 | $0.00104 |
Grade A, and why
agent-skills AGENTS.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.
AGENTS.md
This file provides guidance to coding agents (Claude Code and other Agent Skills-compatible tools) 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 <github-url> [branch] <description>) 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.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/, 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). Covers both process modules and workflow modules (Kind: Workflow).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 Changed · +41 tokens per session d16b09f1c3c2
- 12d ago First seen · 50 lines · 1,004 tokens per session scan A 3724a05474d2
agent-skills AGENTS.md is an instructions file published in the GitHub repository nextflow-io/agent-skills (24 stars, last pushed 6d ago), licensed Apache-2.0. It adds 1,045 tokens to every session, about $0.0042 per session on Opus 5.5. 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 2026-10-08.
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).
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.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).
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.
vscode copilot-instructions.md
Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).
deepseek-harness AGENTS.md
AGENTS.md instructions for deepseek-ai/deepseek-harness, covering agents.md, pre-stable apis and released session data, repository layout, commands and host sandbox failures.