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# nf-hello plugin | ||
# nf-iridanext plugin | ||
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This project contains a simple Nextflow plugin called `nf-hello` which provides examples of different plugin extensions: | ||
This project contains a plugin for integrating Nextflow pipelines with [IRIDA Next][irida-next]. In particular, it will enable a pipeline to produce output consistent with the IRIDA Next [pipeline standards][]. | ||
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- A custom trace observer that prints a message when the workflow starts and when the workflow completes | ||
- A custom channel factory called `reverse` | ||
- A custom operator called `goodbye` | ||
- A custom function called `randomString` | ||
# Credits | ||
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NOTE: If you want to use this project as a starting point for a custom plugin, you must rename the `plugins/nf-hello` folder and update `settings.gradle` with your plugin name. | ||
This plugin was developed based on the `nf-hello` Nextflow plugin template <https://github.com/nextflow-io/nf-hello>. | ||
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## Plugin structure | ||
- `settings.gradle` | ||
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Gradle project settings. | ||
# Legal | ||
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- `plugins/nf-hello` | ||
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The plugin implementation base directory. | ||
Copyright 2023 Government of Canada | ||
Original nf-hello project Copyright to respective authors | ||
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- `plugins/nf-hello/build.gradle` | ||
Plugin Gradle build file. Project dependencies should be added here. | ||
Licensed under the Apache License, Version 2.0 (the "License"); you may not use | ||
this work except in compliance with the License. You may obtain a copy of the | ||
License at: | ||
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- `plugins/nf-hello/src/resources/META-INF/MANIFEST.MF` | ||
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Manifest file defining the plugin attributes e.g. name, version, etc. The attribute `Plugin-Class` declares the plugin main class. This class should extend the base class `nextflow.plugin.BasePlugin` e.g. `nextflow.hello.HelloPlugin`. | ||
http://www.apache.org/licenses/LICENSE-2.0 | ||
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- `plugins/nf-hello/src/resources/META-INF/extensions.idx` | ||
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This file declares one or more extension classes provided by the plugin. Each line should contain the fully qualified name of a Java class that implements the `org.pf4j.ExtensionPoint` interface (or a sub-interface). | ||
Unless required by applicable law or agreed to in writing, software distributed | ||
under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR | ||
CONDITIONS OF ANY KIND, either express or implied. See the License for the | ||
specific language governing permissions and limitations under the License. | ||
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- `plugins/nf-hello/src/main` | ||
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The plugin implementation sources. | ||
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- `plugins/nf-hello/src/test` | ||
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The plugin unit tests. | ||
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## Plugin classes | ||
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- `HelloConfig`: shows how to handle options from the Nextflow configuration | ||
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- `HelloExtension`: shows how to create custom channel factories, operators, and fuctions that can be included into pipeline scripts | ||
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- `HelloFactory` and `HelloObserver`: shows how to react to workflow events with custom behavior | ||
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- `HelloPlugin`: the plugin entry point | ||
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## Unit testing | ||
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To run your unit tests, run the following command in the project root directory (ie. where the file `settings.gradle` is located): | ||
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```bash | ||
./gradlew check | ||
``` | ||
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## Testing and debugging | ||
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To build and test the plugin during development, configure a local Nextflow build with the following steps: | ||
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1. Clone the Nextflow repository in your computer into a sibling directory: | ||
```bash | ||
git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow | ||
``` | ||
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2. Configure the plugin build to use the local Nextflow code: | ||
```bash | ||
echo "includeBuild('../nextflow')" >> settings.gradle | ||
``` | ||
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(Make sure to not add it more than once!) | ||
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3. Compile the plugin alongside the Nextflow code: | ||
```bash | ||
make compile | ||
``` | ||
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4. Run Nextflow with the plugin, using `./launch.sh` as a drop-in replacement for the `nextflow` command, and adding the option `-plugins nf-hello` to load the plugin: | ||
```bash | ||
./launch.sh run nextflow-io/hello -plugins nf-hello | ||
``` | ||
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## Testing without Nextflow build | ||
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The plugin can be tested without using a local Nextflow build using the following steps: | ||
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1. Build the plugin: `make buildPlugins` | ||
2. Copy `build/plugins/<your-plugin>` to `$HOME/.nextflow/plugins` | ||
3. Create a pipeline that uses your plugin and run it: `nextflow run ./my-pipeline-script.nf` | ||
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## Package, upload, and publish | ||
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The project should be hosted in a GitHub repository whose name matches the name of the plugin, that is the name of the directory in the `plugins` folder (e.g. `nf-hello`). | ||
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Follow these steps to package, upload and publish the plugin: | ||
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1. Create a file named `gradle.properties` in the project root containing the following attributes (this file should not be committed to Git): | ||
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* `github_organization`: the GitHub organisation where the plugin repository is hosted. | ||
* `github_username`: The GitHub username granting access to the plugin repository. | ||
* `github_access_token`: The GitHub access token required to upload and commit changes to the plugin repository. | ||
* `github_commit_email`: The email address associated with your GitHub account. | ||
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2. Use the following command to package and create a release for your plugin on GitHub: | ||
```bash | ||
./gradlew :plugins:nf-hello:upload | ||
``` | ||
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3. Create a pull request against [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json) to make the plugin accessible to Nextflow. | ||
[irida-next]: https://github.com/phac-nml/irida-next | ||
[pipeline standards]: https://github.com/phac-nml/pipeline-standards |
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distributionBase=GRADLE_USER_HOME | ||
distributionPath=wrapper/dists | ||
distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip | ||
distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip | ||
zipStoreBase=GRADLE_USER_HOME | ||
zipStorePath=wrapper/dists |
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plugins { | ||
id 'nf-hello' | ||
id 'nf-iridanext' | ||
} |
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plugins/nf-hello/src/main/nextflow/hello/HelloConfig.groovy
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