install-nextflow

# 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 ```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 26.04.0**, 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): ```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 **26.04.0 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: ```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 26.04.0+** — 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`.