They were indeed. Two Mersey passenger ferries manned by volunteers - the 'Daffodil' and the 'Iris II'.
'Daffodil' was charged with pushing HMS 'Vindictive' against the harbour wall to disembark their raiding party assisted by Iris II that I believe had marines on board.
They were part of the diversionary tactic on the Mole at Zeebrugge assisting HMS 'Vindictive' to draw attention from the real objective - to sink three concrete laden block ships in the entrance to the port to prevent German submarines from moving into the North Sea.
http://www.merseyside-at-war.org/memorabilia/iris-and-daffodil/
A more modern warship - HMS 'Somerset' - that berthed in Dover Harbour for the Anniversary Commemorations on 23 April. Here preparing to leave on 25th.