taxprofiler/lib/Utils.groovy

//
// This file holds several Groovy functions that could be useful for any Nextflow pipeline
//

import org.yaml.snakeyaml.Yaml

class Utils {

    //
    // When running with -profile conda, warn if channels have not been set-up appropriately
    //
    public static void checkCondaChannels(log) {
        Yaml parser = new Yaml()
        def channels = []
        try {
            def config = parser.load("conda config --show channels".execute().text)
            channels = config.channels
        } catch(NullPointerException | IOException e) {
            log.warn "Could not verify conda channel configuration."
            return
        }

        // Check that all channels are present
        def required_channels = ['conda-forge', 'bioconda', 'defaults']
        def conda_check_failed = !required_channels.every { ch -> ch in channels }

        // Check that they are in the right order
        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))

        if (conda_check_failed) {
            log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                "  There is a problem with your Conda configuration!\n\n" +
                "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
                "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
                "  NB: The order of the channels matters!\n" +
                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
        }
    }
}