nf-prov

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

Getting Started

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 produce the specified provenance reports at the end of the workflow run.

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

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

• bco: Render a BioCompute Object. Supports the file and overwrite options. See BCO.md for more information about the additional config options for BCO.

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

Deprecated in version 1.4.0

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

New in version 1.4.0

• wrroc: Render a Workflow Run RO-Crate. Includes all three profiles (Process, Workflow, and Provenance). See WRROC.md for more information about the additional config options for WRROC.

Any number of formats can be specified, for example:

prov {
  formats {
    bco {
      file = 'bco.json'
      overwrite = true
    }
    wrroc {
      file = 'ro-crate-metadata.json'
      overwrite = true
    }
  }
}

See the nf-prov-test directory for an example pipeline that produces every provenance format.

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

Build and install the plugin to your local Nextflow installation:

make install

Run with Nextflow as usual:

nextflow run nf-prov-test -plugins nf-prov@<version>

Package, Upload, and Publish

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

1. In build.gradle make sure that:

   • version matches the desired release version,
   • github.repository matches the repository of the plugin,
   • github.indexUrl points to your fork of the plugins index repository.

2. Create a file named $HOME/.gradle/gradle.properties, where $HOME is your home directory. Add the following properties:

   • 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.

3. Update the changelog.

4. Build and publish the plugin to your GitHub repository:

   make release

5. Create a pull request against the nextflow-io/plugins repository to make the plugin publicly accessible.