An action to install Nextflow into a GitHub Actions workflow and make it available for subsequent steps.

name: Example workflow
on: push
jobs:
  example:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6
      - uses: nf-core/setup-nextflow@v2
      - run: nextflow run ${GITHUB_WORKSPACE}

All inputs are optional! 😎 By default, this action will install the latest stable release of Nextflow. You can optionally pick a different version, or choose to install all versions.

default: latest

A version string to specify the version of Nextflow to install. This version number will try to resolve using npm's semantic versioning, so

• version: 21
• version: 21.10
• version: 21.10.6

will all download Nextflow version 21.10.6 as of 13 June 2022. Since Nextflow does not use true semantic versioning, you should always specify at least the minor version (e.g. version: 21.10).

Edge releases are resolved as pre-release, see https://github.com/npm/node-semver#prerelease-tags for more details. In short, in nearly all cases, passing an -edge release to this action will need to specify the exact edge release targeted.

There are three (technically four) aliases to assist in choosing up-to-date Nextflow versions.

• version: latest-stable (alias version: latest)

  This will download the latest stable release of Nextflow.

• version: latest-edge

  This will download the latest edge release of Nextflow. Note that edge releases may be older than the latest stable release. See nextflow-io/nextflow#2467

• version: latest-everything

  This will download the latest release of Nextflow, regardless of stable/edge status.

default: false

A boolean deciding whether to download the "all versions" distribution of Nextflow. May be useful for running tests against multiple versions downstream.

default: true

Nextflow requires Java, so by default this action installs it using actions/setup-java before installing Nextflow.

Set this to false if you provide your own Java installation (for example a pre-installed or self-managed JDK on a self-hosted runner) and want to skip that step:

- uses: nf-core/setup-nextflow@v3
  with:
    install-java: false

When skipping the Java installation, it is up to you to make sure that a Java version supported by Nextflow is available, either via JAVA_HOME or on the PATH. The action checks for one before installing Nextflow and fails with an explanatory error if it can't find any, rather than leaving you with a Nextflow installation that breaks the first time it runs. It does not check which version it found, so a Java that is too old for your chosen Nextflow version is still your responsibility.

default: 17

The Java version to install. Passed to the java-version input of actions/setup-java. Ignored if install-java is false.

default: temurin

The Java distribution to install. Passed to the distribution input of actions/setup-java. Ignored if install-java is false.

default: none

Nextflow secrets to set, specified as KEY=VALUE pairs (one per line). VALUE will only be logged as a masked value. Typically, VALUE will be a GitHub repository secret:

- uses: nf-core/setup-nextflow@v2
  with:
    secrets: |
      MY_SECRET=${{ secrets.MY_GITHUB_SECRET }}
      ANOTHER_SECRET=${{ secrets.ANOTHER_GITHUB_SECRET }}

These are equivalent to running nextflow secrets set MY_SECRET <value> before your workflow steps.

There are no outputs from this action.

Slack link

You may be asking, why not just a few yaml lines?

- name: Install Nextflow
  env:
    NXF_VER: ${{ matrix.NXF_VER }}
  run: |
    wget -qO- get.nextflow.io | bash
    sudo mv nextflow /usr/local/bin/

The versioning. From the Nextflow install script you can't get latest-edge or latest-everything for example.