Having played around a bit I have answered my own question.
I discovered that Nikon Transfer has an option to open another App automatically, so by setting that to Lightroom I have achieved what I wanted.
I'd suggest you use Lightroom and import directly. In Lightroom make sure you're in the Library module, click on the import button on the bottom of the left panel, you'll get an import popup, select where the images are coming from, ( your SD card or camera) then decide whether you wan to copy or copy as a DNG file, then choose where you want to store them on your computer, I suggest the Pictures folder on your harddrive.
Give it a try.
I have tried that but as I said in my original post Lightroom doesn't clear the camera memory after doing the import, whereas Nikon Transfer does. To clear the camera you have to use some other app.
Also in Lightroom you then have to select the source and destination folders which I know is picky but it can be a pain.
Doing it with Nikon Transfer automates the whole process so all you do is connect camera switch it on Nikon Transfer opens one click and it downloads photos to temporary folder then clears the camera memory launches Lightroom with all the new photos selected ready to import and then one more click and they are imported and moved to the subfolder of Pictures you last used.
Thats about as easy as it can be so I am happy.