Refactor repo as agent-skills

.claude-plugin/plugin.json

@@ -1,12 +1,18 @@
 {
   "name": "nextflow",
-  "description": "Nextflow and nf-core bioinformatics workflow skills powered by Seqera MCP",
+  "description": "Nextflow and nf-core bioinformatics workflow skills",
   "version": "1.0.0",
   "author": {
     "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"]
+  "keywords": ["nextflow", "nf-core", "bioinformatics", "seqera", "workflows"],
+  "skills": [
+    "./skills/create-workflow/SKILL.md",
+    "./skills/install-nextflow/SKILL.md",
+    "./skills/launch-workflow/SKILL.md",
+    "./skills/run-module/SKILL.md"
+  ]
 }

README.md

@@ -1,44 +1,27 @@
-# Nextflow Claude Code Plugin
+# Nextflow Agent Skills
 
-Claude Code skills for Nextflow and nf-core bioinformatics workflows, powered by the Seqera MCP server.
+[![skills.sh](https://skills.sh/b/nextflow-io/agent-skills)](https://skills.sh/nextflow-io/agent-skills)
+
+Agent skills for Nextflow and nf-core bioinformatics workflows.
 
 ## 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
-
-```bash
-/plugin marketplace add nextflow-io/claude-plugin
-```
-
-### 2. Install the plugin
+Install the skills with [`skills.sh`](https://skills.sh):
 
 ```bash
-/plugin install nextflow@nextflow-io-claude-plugin
+npx skills@latest add 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.
-
-## Usage
-
-Once installed, use the skills with the `nextflow:` namespace:
-
-```bash
-/nextflow:install-nextflow
-/nextflow:create-workflow
-/nextflow:run-module
-/nextflow:launch-workflow
-```
+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.
 
 ## Local Development
 
@@ -50,8 +33,8 @@ 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
 

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.**
 

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
 
@@ -127,9 +127,9 @@ Confirm the reported version is **26.04.0 or later**. Present the version to the
 Stable Nextflow releases use **calendar versioning** in the form `YY.MM.PATCH`:
 
 - `25.10.1` — patch 1 of the October 2025 release
-- `26.04.0` — first release of April 2026
+- `26.04` — first release of April 2026
 
-Compare versions as calendar dates, not semver — `26.04.0` is newer than `25.10.1`.
+Compare versions as calendar dates, not semver — `26.04` is newer than `25.10.1`.
 
 ### Edge releases
 
@@ -160,11 +160,11 @@ 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.
 6. **REMEMBER stderr** — `java -version` writes to stderr; redirect with `2>&1` when parsing.
 7. **VERIFY at the end** — always run `nextflow -version` after install/upgrade to confirm the result.
 8. **USE NXF_VER for pinning** — when the user asks for a specific Nextflow version, set `NXF_VER` instead of reinstalling.
-9. **TREAT versions as calendar dates** — Nextflow uses `YY.MM.PATCH`, not semver, so `26.04.0` is newer than `25.10.1`.
+9. **TREAT versions as calendar dates** — Nextflow uses `YY.MM.PATCH`, not semver, so `26.04` is newer than `25.10.1`.

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
 

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