stefanches7 / nf-prov

nf-prov

Nextflow plugin to render provenance reports for pipeline runs. Now supporting BioCompute Objects!

Getting Started

The nf-prov plugin requires Nextflow version 23.04.0 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
  formats {
    legacy {
      file = 'manifest.json'
      overwrite = true
    }
  }
}

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.

Configuration

The file, format, and overwrite options have been deprecated since version 1.2.0. Use formats instead.

The following options are available:

prov.enabled

Create the provenance report (default: true if plugin is loaded).

prov.formats

New in version 1.2.0

Configuration scope for the desired output formats. The following formats are available:

• bco: Render a BioCompute Object. Supports the file and overwrite options.

  Visit the BCO User Guide to learn more about this format and how to extend it with information that isn't available to Nextflow.

• dag: Render the task graph as a Mermaid diagram embedded in an HTML document. Supports the file and overwrite options.

• legacy: Render the legacy format originally defined in this plugin (default). Supports the file and overwrite options.

Any number of formats can be specified, for example:

prov {
  formats {
    bco {
      file = 'bco.json'
      overwrite = true
    }
    legacy {
      file = 'manifest.json'
      overwrite = true
    }
  }
}

prov.patterns

List of file patterns to include in the provenance report, from the set of published files. By default, all published files are included.

Development

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

# Prepare the nextflow repo
cd ../nextflow && ./gradlew compile exportClasspath && cd -

# Prepare the nf-prov repo
grep -v 'includeBuild' settings.gradle > settings.gradle.bkp
echo "includeBuild('../nextflow')" >> settings.gradle.bkp
mv -f settings.gradle.bkp settings.gradle
./gradlew assemble

# Launch
./launch.sh run test.nf -plugins nf-prov

Package, Upload, and Publish

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-prov in this project.

Following these step to package, upload and publish the plugin:

1. 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 hosted
• github_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.

2. Update the Plugin-Version field in the following file with the release version:

   plugins/nf-prov/src/resources/META-INF/MANIFEST.MF

3. Run the following command to package and upload the plugin in the GitHub project releases page:

   ./gradlew :plugins:nf-prov:upload

4. Create a pull request against the nextflow-io/plugins project to make the plugin public accessible to Nextflow app.