Summary

Nextflow plugin to render provenance reports for pipeline runs. Supports standard formats such as BioCompute Object and Workflow Run RO-Crate.

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

Any number of formats can be specified. You do not need to modify your pipeline script in order to use the nf-prov plugin.

When you run your Nextflow pipeline, the plugin will automatically produce the specified provenance reports at the end of the run.

Configuration

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

The legacy format was removed in version 1.5.0. Consider using data lineage instead.

The following options are available:

prov.directory

New in version 1.8.0

The directory where the provenance reports should be saved. The path is resolved against the workflow output directory (outputDir). It must be a relative path within the output directory, and it cannot be used when a report file is an absolute path. By default, it is not used and report files are resolved against the launch directory.

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.

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.

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

New in version 1.7.0

• gexf: Render the workflow run as a GEXF document. Supports the file and overwrite options.

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.

Examples

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

License

This project is licensed under the Apache License 2.0.