Run up river as punishment (7)
I believe the answer is:
torture
'punishment' is the definition.
(thesaurus)
'run up river' is the wordplay.
'run' becomes 'trot' (trotting is a kind of running).
'up' shows that the letters should be reversed in order (in down clue: letters go upwards).
'river' becomes 'ure' (river in Yorkshire).
'trot' written backwards gives 'tort'.
'tort'+'ure'='TORTURE'
'as' acts as a link.
(Other definitions for torture that I've seen before include "Inflict great suffering" , "Torment" , "Infliction of physical or mental suffering" , "Inflict pain to extract information" , "cause extreme discomfort?" .)