Rubbish runs through part of ship (5)
I believe the answer is:
dreck
'rubbish' is the definition.
(I've seen this in another clue)
'runs through part of ship' is the wordplay.
'runs' becomes 'r' (cricket abbreviation).
'through' indicates putting letters inside (inserted letters go through the word).
'part of ship' becomes 'deck' ('deck' is part of 'ship').
'r' placed inside 'deck' is 'DRECK'.
(Other definitions for dreck that I've seen before include "Rubbish" , "Refuse" .)