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41 lines
1.7 KiB
Groovy
41 lines
1.7 KiB
Groovy
//
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// This file holds several Groovy functions that could be useful for any Nextflow pipeline
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//
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import org.yaml.snakeyaml.Yaml
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class Utils {
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//
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// When running with -profile conda, warn if channels have not been set-up appropriately
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//
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public static void checkCondaChannels(log) {
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Yaml parser = new Yaml()
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def channels = []
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try {
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def config = parser.load("conda config --show channels".execute().text)
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channels = config.channels
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} catch(NullPointerException | IOException e) {
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log.warn "Could not verify conda channel configuration."
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return
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}
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// Check that all channels are present
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def required_channels = ['conda-forge', 'bioconda', 'defaults']
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def conda_check_failed = !required_channels.every { ch -> ch in channels }
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// Check that they are in the right order
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conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
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conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
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if (conda_check_failed) {
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log.warn "=============================================================================\n" +
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" There is a problem with your Conda configuration!\n\n" +
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" You will need to set-up the conda-forge and bioconda channels correctly.\n" +
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" Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
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" NB: The order of the channels matters!\n" +
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"==================================================================================="
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}
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}
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}
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