Plugin references both monochrome_logs and monochromeLogs

[Midnighter]

The plugin configures its own logging using nf-core conventions. For this it uses both parameters monochrome_logs and monochromeLogs. I assume the latter is supported for backwards compatibility. However, the current code creates a slightly annoying warning (as in, the warning may confuse users who don't know what it means).

WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

I looked a bit in the code and I think it must be triggered by the containsKey method on line 248 in the SchemaValidator.groovy file, since you set the value afterwards, which I guess was intended to avoid exactly this.

        if( !params.containsKey("monochromeLogs") ) {
            params.monochromeLogs = false
        }

Alternatively, setting the value does not work as expected such that it is still null in the outer scope.

I'm, unfortunately, not familiar with the gradle build tools and testing, otherwise I could work on a fix myself. One suggestion would be to use the session.params, to initialize the plugin's own settings (which can be more or less a copy), rather than continuing to use those for checks.

[nvnieuwk]

This problem has been solved by moving to the validation.monochromeLogs configuration option instead in nf-schema