Fix bug in unexpected param log with false values.

[ewels]

Follow-on to #857

Tried to add params.input_paths = null to nextflow.config to avoid the warning that Nextflow threw about undefined params and hit a bug in the new unexpected params code:

JSONObject["input_paths"] not found.
 -- Check script 'nf-core-test/main.nf' at line: 28 or see '.nextflow.log' file for more details

After a bit of digging I figured out that it was because this code was removing anything evaluating to false from the parameters map:

tools/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/lib/NfcoreSchema.groovy

Lines 197 to 200 in 729f03a

	// remove anything evaluating to false
	if (!p['value']) {
	new_params.remove(p.key)
	}

So just switching to use params instead of cleanedParams when printing the value of the unexpected parameter solved the issue.

Also included a couple of other minor tweaks, notably just repeating the validation at the end of the pipeline. This is so that we don't have to repeat the code that prints the warnings so a bit less code maintenance in the main pipeline.

[KevinMenden]

Nice fix, thanks! :)

Was thinking if it makes sense to force the second call to validateParams to print unexpected params? But then a user can't really switch it off so maybe best to leave it like this 👍