mirror of
https://github.com/MillironX/setup-nextflow.git
synced 2024-12-22 21:08:16 +00:00
82 lines
3.5 KiB
Markdown
82 lines
3.5 KiB
Markdown
#  
|
|
|
|
[](https://github.com/nf-core/setup-nextflow/actions/workflows/example.yml)
|
|
[](https://codecov.io/gh/nf-core/setup-nextflow)
|
|
[](https://github.com/nf-core/setup-nextflow/blob/master/LICENSE)
|
|
[](https://github.com/nf-core/setup-nextflow/releases/latest)
|
|
[](https://github.com/marketplace/actions/setup-nextflow)
|
|
|
|
An action to install [Nextflow](https://nextflow.io) into a GitHub Actions workflow and make it available for subsequent steps.
|
|
|
|
## Quick start
|
|
|
|
```yaml
|
|
name: Example workflow
|
|
on: push
|
|
jobs:
|
|
example:
|
|
runs-on: ubuntu-latest
|
|
steps:
|
|
- uses: actions/checkout@v3
|
|
- uses: nf-core/setup-nextflow@v1
|
|
- run: nextflow run ${GITHUB_WORKSPACE}
|
|
```
|
|
|
|
## Inputs
|
|
|
|
All inputs are optional! :sunglasses: By default, this action will install the [latest stable release](https://nextflow.io/docs/latest/getstarted.html#stable-edge-releases) of Nextflow. You can optionally pick a different version, or choose to install all versions.
|
|
|
|
### `version`
|
|
|
|
> **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](https://github.com/npm/node-semver), 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 https://github.com/nextflow-io/nextflow/issues/2467
|
|
|
|
- `version: latest-everything`
|
|
|
|
This will download the latest release of Nextflow, regardless of stable/edge status.
|
|
|
|
### `all`
|
|
|
|
> **default: `false`**
|
|
|
|
A boolean deciding whether to download the "all versions" distribution of Nextflow. May be useful for running tests against multiple versions downstream.
|
|
|
|
## Outputs
|
|
|
|
There are no outputs from this action.
|
|
|
|
## Why was this action made?
|
|
|
|
[Slack link](https://nfcore.slack.com/archives/CE56GDKN0/p1655210460795839)
|
|
|
|
You may be asking, why not just a few yaml lines?
|
|
|
|
```yaml
|
|
- 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.
|