The following snippet fails because the Closure of the LineFilter returns an empty String:

task setupScripts(type:Copy){
	from "/Users/Rene/workspaces/gradle/samples"
	into "gradlesamples"
	filter{line ->
		if(line.contains("IGNORE_ME")){
			return ""
		}
		line
	}
}

I've attached a modified LineFilterTest class with an additional test for this scenario.