The nf-prov Nextflow plugin

Nextflow is a computational workflow manager that enables the development of complex pipelines by composing many simple processes. nf-prov is a Nextflow plugin to generate provenance information for pipeline runs. It supports serialization in the BioCompute Object and Workflow Run RO-Crate (WRROC) formats. WRROC support is available since version 1.4.0 of the plugin.

To enable RO-Crate generation, add the following to the Nextflow configuration:

plugins {
    id 'nf-prov@1.4.0'
}

prov {
    enabled = true
    formats {
        wrroc {
            file = "${params.outdir}/ro-crate-metadata.json"
            overwrite = true
            agent {
                name = "Jane Doe"
                orcid = "https://orcid.org/0000-0000-0000-0000"
            }
            license = "https://spdx.org/licenses/MIT"
        }
    }
}

The above snippet is just an example. To get an overview of the available configuration options, check out the documentation for the WRROC format.

To try the plugin, move to an empty directory and save the above snippet to a file called nextflow.config. Then run:

nextflow run rnaseq-nf -profile docker --outdir results

The results directory will contain the pipeline output and an ro-crate-metadata.json file with the RO-Crate metadata.

Other RO-Crate support in Nextflow

The nf-core RO-Crate tool can generate a Workflow Testing RO-Crate for a Nextflow pipeline. Workflow Testing RO-Crate is a specialization of Workflow RO-Crate that supports additional metadata related to the testing of computational workflows, allowing workflows to be automatically tested and monitored by the LifeMonitor service.

The nf-core RO-Crate tool utilises the repo2rocrate library, which also supports Galaxy and Snakemake.

The nf-prov Nextflow plugin

Other RO-Crate support in Nextflow

Resources