install-nextflow

name	install-nextflow
description	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.
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.

Step 1: Check Whether Nextflow Is Installed

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 26.04.0, the user MUST upgrade — this plugin's 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):

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:

java -version

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

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:

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

If SDKMAN is missing, install it:

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

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

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

After installation, verify:

java -version

Step 4: Install Nextflow

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

Detect which downloader is available:

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

Using curl:

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

Using wget (if curl is missing):

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):

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

nextflow -version

Confirm the reported version is 26.04.0 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:

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:

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 26.04.0+ — the plugin's other 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.