# Install Nextflow

> Install or upgrade Nextflow on the user's machine. Use when the user wants to install Nextflow, check their current Nextflow version, upgrade Nextflow, or set up the prerequisites (Java 17+) needed to run Nextflow.

- Skill: `nextflow-io/install-nextflow` (Agent Skill)
- Install (CLI): `npx skillmds@latest add nextflow-io/install-nextflow`
- Raw SKILL.md: https://api.skillmd.com/api/skills/nextflow-io/install-nextflow/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: nextflow-io (https://skillmd.com/u/nextflow-io)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/nextflow-io/install-nextflow

---


# Install or Upgrade Nextflow

Install Nextflow (or upgrade an existing installation) and ensure the Java prerequisite is in place.

## Step 1: Check Whether Nextflow Is Installed

```bash
command -v nextflow && nextflow -version
```

- **If installed**, parse the version from the output and proceed to Step 2.
- **If not installed**, skip to Step 3.

## Step 2: Check for Upgrades (Existing Install)

If Nextflow is already installed:

1. Read the installed version from `nextflow -version`.
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):

```bash
nextflow self-update
```

Confirm with the user before running it. After the update, re-run `nextflow -version` to verify.

If the install is already up to date, stop here.

## Step 3: Verify Java 17+ (Required for Installing Nextflow)

Nextflow requires Java 17 or later. Check the installed Java version:

```bash
java -version
```

Note: `java -version` writes to **stderr**, not stdout. Capture both streams when parsing:

```bash
java -version 2>&1 | head -1
```

- If Java 17+ is present, proceed to Step 4.
- If Java is missing or older than 17, install Java 21 using SDKMAN (Step 3a).

### Step 3a: Install Java 21 via SDKMAN

First, check whether SDKMAN is installed:

```bash
[ -s "$HOME/.sdkman/bin/sdkman-init.sh" ] && echo "SDKMAN present" || echo "SDKMAN missing"
```

If SDKMAN is missing, install it:

```bash
curl -s "https://get.sdkman.io" | bash
```

Then load SDKMAN into the current shell session and install Java 21:

```bash
source "$HOME/.sdkman/bin/sdkman-init.sh"
sdk install java 21-tem
```

After installation, verify:

```bash
java -version
```

## Step 4: Install Nextflow

Prefer `curl`; fall back to `wget` if `curl` is unavailable.

Detect which downloader is available:

```bash
command -v curl >/dev/null && echo "curl" || (command -v wget >/dev/null && echo "wget" || echo "none")
```

**Using curl:**

```bash
curl -fsSL https://get.nextflow.io | bash
```

**Using wget (if curl is missing):**

```bash
wget -qO- https://get.nextflow.io | bash
```

If neither `curl` nor `wget` is available, stop and ask the user to install one of them.

The installer drops a `nextflow` launcher in the current directory. Move it onto the user's `PATH` (confirm the destination with the user first):

```bash
chmod +x nextflow
mv nextflow ~/.local/bin/
```

Common alternatives are `/usr/local/bin/` (may need `sudo`) or any directory already on `PATH` (`echo $PATH`).

## Step 5: Verify the Installation

```bash
nextflow -version
```

Confirm the reported version is **26.04 or later**. Present the version to the user.

## Nextflow Versioning

### Calendar versioning

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

Compare versions as calendar dates, not semver — `26.04.0` is newer than `25.10.1`.

### Edge releases

Edge (preview) releases append the `-edge` suffix, e.g. `26.05.0-edge`. They include unreleased features and are not recommended for production.

Switch the active channel via the `NXF_EDGE` environment variable:

```bash
export NXF_EDGE=1   # use edge releases
export NXF_EDGE=0   # back to stable releases (default)
```

This affects which release `nextflow self-update` and the launcher resolve to.

### Pinning a specific version

Pin any version (stable or edge) with `NXF_VER`. The launcher will download and use that exact version on the next run:

```bash
export NXF_VER=25.10.1        # pin a stable release
export NXF_VER=26.05.0-edge   # pin an edge release
```

Unset `NXF_VER` (`unset NXF_VER`) to return to the latest version of the active channel.

When the user asks to install or run a specific version, set `NXF_VER` rather than reinstalling.

## Critical Rules

1. **CHECK FIRST** — always run `nextflow -version` before deciding to install or upgrade.
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`.