To get this done without adding any user written transformation and perhaps elegantly you can try what i generally use. First, copy the numobs macro posted by @cmjohns ( https://stackoverflow.com/a/5664379/4653284 ) and add it to the precode of the jobflow.
After that go to the starting transformation which needs to be skipped based on the observation and right click to get properties tab of that transformation. Then goto the "Precode and Postcode" tab and add the following code:
%macro dummy;
%if %nobs(&SYSLAST) gt 0 %then %do;
After that is done, goto the transformation which would be the last transformation to be skipped basis the observation count and right click to get properties of the transformation and goto Precode Postcode tab and add the following code:
%end;
%mend dummy;
%dummy;
If only 1 transformation needs to be skipped then you can add the post code and precode provided above in the same precode and post code tab of that single transformation to skip it based on observation count.
Note: SAS DI Studio 4.8 has Conditional Transformations which can solve the same problem. But for DI studio version before that we have to code to get the conditional exclusion of transformation(s).