Use the transformations Conditional Start and Conditional Start, you can find them in the Transformations under Control.
The condition specified in Conditional Start is a macro expression, so either in a step before or in the precode of Conditional Start, enter the code that will create the macro variable. Example:
%let Rows=0;
proc sql noprint;
select count(*) into : Rows trimmed
from &_INPUT1 ;
quit;
the above example will only work with a User Written Transformation using the output table from Step 3 as input.
In your Conditional Start the condition would then be: &Rows > 0