This plugin implements a Nextflow executor for Hashicorp Nomad.
Please note that this is a community contributed plugin and is a collaboration between
- Abhinav Sharma (@abhi18av) as part of his PhD work at the Stellenbosch University
- Matthias de Smet (@matthdsm) and Tomas (@tomiles) from Center For Medical Genetics Ghent
Feel free to reach out to us on the #platform-nomad
channel on Slack for discussions and feedbacks.
-
settings.gradle
Gradle project settings.
-
plugins/nf-nomad
The plugin implementation base directory.
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plugins/nf-nomad/build.gradle
Plugin Gradle build file. Project dependencies should be added here.
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plugins/nf-nomad/src/resources/META-INF/MANIFEST.MF
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 classnextflow.plugin.BasePlugin
e.g.nextflow.Nomad.NomadPlugin
. -
plugins/nf-nomad/src/resources/META-INF/extensions.idx
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). -
plugins/nf-nomad/src/main
The plugin implementation sources.
-
plugins/nf-nomad/src/test
The plugin unit tests.
ExtensionPoint
is the basic interface which uses nextflow-core to integrate plugins into it. It's only a basic interface and serves as starting point for more specialized extensions.
Run the following command in the project root directory (ie. where the file settings.gradle
is located):
./gradlew check
To run and test the plugin in a development environment, configure a local Nextflow build with the following steps:
-
Clone the Nextflow repository in your computer into a sibling directory:
git clone --depth 1 https://github.com/nextflow-io/nextflow _resources/nextflow
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Generate the nextflow class path
cd _resources/nextflow && ./gradlew exportClasspath
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Compile the plugin alongside the Nextflow code:
cd ../../ && ./gradlew compileGroovy
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Run Nextflow with the plugin, using
./launch.sh
as a drop-in replacement for thenextflow
command, and adding the option-plugins nf-nomad
to load the plugin:./launch.sh run main.nf -plugins nf-nomad
The project should be hosted in a GitHub repository whose name should match the name of the plugin, that is the name of the directory in the plugins
folder (e.g. nf-nomad
).
Follow these steps to package, upload and publish the plugin:
-
Create a file named
gradle.properties
in the project root containing the following attributes (this file should not be committed to Git):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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Use the following command to package and create a release for your plugin on GitHub:
./gradlew :plugins:nf-nomad:upload
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Create a pull request against nextflow-io/plugins to make the plugin accessible to Nextflow.