nextflow-io · bentsherman · May 20, 2026 · May 20, 2026 · May 29, 2026 · May 29, 2026
diff --git a/.claude-plugin/plugin.json b/.claude-plugin/plugin.json
@@ -6,7 +6,7 @@
     "name": "Nextflow",
     "url": "https://nextflow.io"
   },
-  "repository": "https://github.com/nextflow-io/claude-plugin",
+  "repository": "https://github.com/nextflow-io/agent-skills",
   "license": "Apache-2.0",
   "keywords": ["nextflow", "nf-core", "bioinformatics", "seqera", "workflows"]
 }
diff --git a/README.md b/README.md
@@ -1,43 +1,48 @@
-# Nextflow Claude Code Plugin
+# Nextflow Agent Skills
 
-Claude Code skills for Nextflow and nf-core bioinformatics workflows, powered by the Seqera MCP server.
+Agent skills for Nextflow and nf-core bioinformatics workflows.
+
+These skills follow the [Agent Skills](https://agentskills.io/specification) specification, so they can be used by any skills-compatible agent, including Claude Code, Codex CLI, OpenCode, and Cursor.
 
 ## Skills
 
-| Skill | Description |
-|-------|-------------|
-| `install-nextflow` | Install or upgrade Nextflow (and Java 17+ via SDKMAN if needed) |
-| `create-workflow` | Create Nextflow pipelines by composing nf-core modules |
-| `run-module` | Run Nextflow modules natively using `nextflow module` commands |
-| `launch-workflow` | Launch workflow executions on Seqera Platform |
+- [`install-nextflow`](./skills/install-nextflow) — Install or upgrade Nextflow (and Java 17+ via SDKMAN if needed)
+- [`create-workflow`](./skills/create-workflow) — Create Nextflow pipelines by composing nf-core modules
+- [`run-module`](./skills/run-module) — Run Nextflow modules natively using the `nextflow module` command
+- [`launch-workflow`](./skills/launch-workflow) — Launch workflow executions on Seqera Platform
 
 ## Installation
 
-### 1. Add the marketplace
+### Claude Code
 
-```bash
-/plugin marketplace add nextflow-io/claude-plugin
 ```
 
-### 2. Install the plugin
+/plugin marketplace add nextflow-io/agent-skills
+/plugin install nextflow@nextflow-io-agent-skills
+```
+
+When prompted, approve the Seqera MCP server connection to enable the skills. Claude Code automatically keeps your skills up to date.
+
+### GitHub CLI
+
+If you use the [GitHub CLI](https://cli.github.com/) (v2.90.0+), you can install skills with [`gh skill`](https://github.blog/changelog/2026-04-16-manage-agent-skills-with-github-cli/):
 
 ```bash
-/plugin install nextflow@nextflow-io-claude-plugin
+gh skill install nextflow-io/agent-skills
 ```
 
-### 3. Approve the Seqera MCP server
+Pick the skills you want and the coding agents you want to install them on. The installer supports Claude Code, Codex, Cursor, and other agents that follow the skills convention.
 
-When prompted, approve the Seqera MCP server connection to enable the skills.
+For skills that require the Seqera MCP (e.g. `launch-workflow`), make sure the [Seqera MCP server](https://mcp.seqera.io/mcp) is configured for your agent.
 
-## Usage
-
-Once installed, use the skills with the `nextflow:` namespace:
+You can update installed skills using `gh skill update`:
 
 ```bash
-/nextflow:install-nextflow
-/nextflow:create-workflow
-/nextflow:run-module
-/nextflow:launch-workflow
+# Check for updates interactively
+gh skill update
+
+# Update all installed skills
+gh skill update --all
 ```
 
 ## Local Development
@@ -50,8 +55,8 @@ claude --plugin-dir /path/to/claude-plugin
 
 ## Requirements
 
-- [Claude Code](https://claude.ai/code) CLI
-- [Nextflow](https://nextflow.io) **26.04.0 or later** (required for `nextflow module` and `nextflow auth`/`nextflow launch` commands)
+- A coding agent that supports agent skills (e.g. Claude Code, Codex, Cursor)
+- [Nextflow](https://nextflow.io) **26.04 or later** (you can use the `install-nextflow` skill to install it)
 
 ## License
 

diff --git a/skills/create-workflow/SKILL.md b/skills/create-workflow/SKILL.md
@@ -11,7 +11,7 @@ allowed-tools: Bash, Read, Edit, Write, Glob, Grep, Skill
 
 Create complete Nextflow workflows by composing validated nf-core modules.
 
-**Requires Nextflow 26.04.0 or later** (for the `nextflow module` commands used during validation).
+**Requires Nextflow 26.04 or later** (for the `nextflow module` commands used during validation).
 
 **NEVER write a wrapper workflow just to run/test a single nf-core module.**
 

diff --git a/skills/install-nextflow/SKILL.md b/skills/install-nextflow/SKILL.md
@@ -6,7 +6,7 @@ allowed-tools: Bash, Read
 
 # Install or Upgrade Nextflow
 
-Install Nextflow (or upgrade an existing installation) and ensure the Java prerequisite is in place. The plugin requires **Nextflow 26.04.0 or later**.
+Install Nextflow (or upgrade an existing installation) and ensure the Java prerequisite is in place.
 
 ## Step 1: Check Whether Nextflow Is Installed
 
@@ -22,7 +22,7 @@ command -v nextflow && nextflow -version
 If Nextflow is already installed:
 
 1. Read the installed version from `nextflow -version`.
-2. If the installed version is **older than 26.04.0**, the user MUST upgrade — this plugin's skills depend on it.
+2. If the installed version is **older than 26.04**, the user MUST upgrade — other Nextflow skills depend on it.
 3. Otherwise, propose an upgrade only if a newer version is available.
 
 Run a self-update (it checks the latest release and updates if newer):
@@ -118,7 +118,7 @@ Common alternatives are `/usr/local/bin/` (may need `sudo`) or any directory alr
 nextflow -version
 ```
 
-Confirm the reported version is **26.04.0 or later**. Present the version to the user.
+Confirm the reported version is **26.04 or later**. Present the version to the user.
 
 ## Nextflow Versioning
 
@@ -160,7 +160,7 @@ When the user asks to install or run a specific version, set `NXF_VER` rather th
 ## Critical Rules
 
 1. **CHECK FIRST** — always run `nextflow -version` before deciding to install or upgrade.
-2. **REQUIRE 26.04.0+** — the plugin's other skills depend on `nextflow module`, `nextflow auth`, and `nextflow launch`, which require this version.
+2. **REQUIRE 26.04+** — other Nextflow skills depend on `nextflow module`, `nextflow auth`, and `nextflow launch`, which require this version.
 3. **VERIFY JAVA 17+** before installing Nextflow — install Java 21 via SDKMAN if missing or too old.
 4. **CONFIRM destructive actions** — ask the user before running `nextflow self-update`, installing SDKMAN, or moving the `nextflow` launcher to a system directory.
 5. **PREFER curl, FALL BACK to wget** — if neither is available, stop and ask the user to install one.

diff --git a/skills/launch-workflow/SKILL.md b/skills/launch-workflow/SKILL.md
@@ -8,7 +8,7 @@ allowed-tools: Bash, Read, Glob, mcp__seqera__search_seqera_api, mcp__seqera__ca
 
 Launch Nextflow pipeline executions on cloud (AWS, Google Cloud, Azure) and HPC clusters (Slurm, LSF, etc.) through Seqera Platform. Seqera Platform manages the target compute environment, executes the pipeline from a remote Git repository, and provides monitoring.
 
-**Requires Nextflow 26.04.0 or later** (for the `nextflow auth` and `nextflow launch` commands).
+**Requires Nextflow 26.04 or later** (for the `nextflow auth` and `nextflow launch` commands).
 
 ## Main Flow
 
@@ -22,7 +22,7 @@ Launch Nextflow pipeline executions on cloud (AWS, Google Cloud, Azure) and HPC
 Check whether the user is already authenticated:
 
 ```bash
-nextflow auth list
+nextflow auth status
 ```
 
 If not authenticated, sign in:
@@ -138,7 +138,7 @@ nextflow launch https://github.com/nf-core/rnaseq \
 
 ## Critical Rules
 
-1. **AUTHENTICATE first** — check `nextflow auth list` before attempting to launch.
+1. **AUTHENTICATE first** — check `nextflow auth status` before attempting to launch.
 2. **CONFIRM the compute environment** — always show the user the selected CE before launching.
 3. **REQUIRE a remote Git repository** — the pipeline must be hosted on GitHub or a compatible Git host. If not, help the user set it up before launching.
 4. **PUSH local changes first** — the launched run uses the remote code, so local edits must be committed and pushed.

diff --git a/skills/run-module/SKILL.md b/skills/run-module/SKILL.md
@@ -8,7 +8,7 @@ allowed-tools: Bash, Read, Glob
 
 Run modules natively using `nextflow module` commands. Everything is self-contained — no external tools or MCP needed. Modules are installed on-the-fly when run.
 
-**Requires Nextflow 26.04.0 or later** (for the `nextflow module` commands).
+**Requires Nextflow 26.04 or later** (for the `nextflow module` commands).
 
 ## ⛔ NEVER WRITE WRAPPER WORKFLOWS