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Version 3.0.0 migration guide

Changes to automatic help messages

Version 3.0.0 removed support for help messages to be automatically generated when validation.help.enabled has been set to true. The main reason for this was that the help message would only get generated at the start of the workflow, which was really flaky and prone to throw errors before the help message ever got printed.

The only way to print help messages now is to use the paramsHelp() function. Ideally this function gets executed as early as possible in the workflow code.

The validation.help.enabled configuration option has been removed from nf-schema and does no longer serve any purpose. This can be safely removed from all configs.

Changes to paramsHelp()

The paramsHelp() function no longer takes an optional positional argument. Please use the new parameter option of the function to provide a specific parameter to print the help message of.

log.info paramsHelp('input')

log.info paramsHelp(parameter: 'input')

Changes to paramsSummaryMap and paramsSummaryLog

The paramsSummaryMap and paramsSummaryLog function no longer take the workflow object as their input. This object is now automatically fetched from the running session.

paramsSummaryMap(workflow)
paramsSummaryLog(workflow)

paramsSummaryMap()
paramsSummaryLog()

Removal of validation.failUnrecognisedParams and validation.failUnrecognisedHeaders

These options were already deprecated since version 2.5.0 and have now been fully removed. The logic behind it will thus no longer work. You can migrate to the new validation.logging configuration options.

validation {
    failUnrecognisedHeaders = true
    failUnrecognisedParams = true
}

validation {
    logging {
        unrecognisedHeaders = 'error'
        unrecognisedParams = 'error'
    }
}