Summary

Collect CLI tool version information from Nextflow processes and collate it for MultiQC. Version strings are bash echo commands designed for use with Nextflow's eval output directive. They produce YAML-formatted lines that MultiQC can read directly. These helpers avoid the need to continuously and verbosely specify version strings in both script and stub blocks.

Get Started

Add the plugin to your Nextflow config:

plugins { id 'nf-versions' }

Examples

Version Functions in Nextflow Processes

include { bwaMem2Version; samtoolsVersion } from 'plugin/nf-versions'

process ALIGN {
    output:
    eval({bwaMem2Version()}), topic: "versions"
    eval({samtoolsVersion()}), topic: "versions"

    script:
    """
    bwa-mem2 mem ... | samtools sort ...
    """
}

Custom Python Libraries and Tools

include { pyPackageVersion } from 'plugin/nf-versions'

process SECRET_SAUCE {
    output:
    eval({pyPackageVersion("secret_sauce_lib")}), topic: "versions"

    script:
    """
    secret-sauce.py ...
    """
}

Custom R Libraries

include { rLibraryVersion } from 'plugin/nf-versions'

process RUN_ICHORCNA {
    output:
    eval({rLibraryVersion("ichorCNA")}), topic: "versions"

    script:
    """
    runIchorCNA.R ...
    """
}

Collating Versions for MultiQC

include { MULTIQC } from './modules/multiqc'
include { collateVersions } from 'plugin/nf-versions'

workflow {
    // ... pipeline logic ... //

    def qc = channel.empty()
    qc = qc.mix(channel.topic("for_multiqc"))
    qc = qc.mix(collateVersions(channel.topic("versions")))

    MULTIQC(qc.collect())
}

License

This plugin is published under the MIT license. Copyright © 2026 Fulcrum Genomics LLC.