Nextflow plugin for tracking provenance of pipeline output files.
The nf-prov
plugin requires Nextflow version 22.11.0-edge
or later.
To enable and configure nf-prov
, include the following snippet to your Nextflow config and update as needed.
plugins {
id 'nf-prov'
}
prov {
enabled = true
overwrite = true
file = "${params.outdir}/manifest.json"
}
Finally, run your Nextflow pipeline. You do not need to modify your pipeline script in order to use the nf-prov
plugin. The plugin will automatically generate a JSON file with provenance information.
The following options are available:
prov.enabled
Create the provenance manifest (default: true
if plugin is loaded).
prov.file
The path of the provenance manifest (default: manifest.json
).
prov.patterns
List of file patterns to include in the provenance manifest, from the set of published files. By default, all published files are included.
prov.overwrite
Overwrite any existing provenance report with the same name (default: false
).
Run the following commands to build and test the nf-prov Nextflow plugin. Refer to the nf-hello README for additional instructions (e.g. for publishing the plugin).
# (Optional) Checkout relevant feature branch
# git checkout <branch>
# Create an empty folder for nf-prov and nextflow repos
git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow-nf-prov
# Prepare the nextflow repo
cd ../nextflow-nf-prov && ./gradlew compile exportClasspath && cd -
# Prepare the nf-prov repo
grep -v 'includeBuild' settings.gradle > settings.gradle.bkp
echo "includeBuild('../nextflow-nf-prov')" >> settings.gradle.bkp
mv -f settings.gradle.bkp settings.gradle
./gradlew assemble
# Launch
./launch.sh run test.nf -plugins nf-prov
The project should 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-synapse
in this project.
Following these step 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 in the project repository):
github_organization
: the GitHub organisation the plugin project is hostedgithub_username
The GitHub username granting access to the plugin project.github_access_token
: The GitHub access token required to upload and commit changes in the plugin repository.github_commit_email
: The email address associated with your GitHub account.
-
Update the
Plugin-Version
field in the following file with the release version:plugins/nf-prov/src/resources/META-INF/MANIFEST.MF
-
Run the following command to package and upload the plugin in the GitHub project releases page:
./gradlew :plugins:nf-prov:upload
-
Create a pull request against the nextflow-io/plugins project to make the plugin public accessible to Nextflow app.