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The reason you're not able to add the second IF is that a subjob in Talend has one starting point. And having connected via the top IF to the tFileInput, you implicitly defined that tFileInput as the input data flow or row. You'll notice that the row from the tFileInput is Main and the other one in the bottom is Lookup - for the tMap.
To achieve your design, you'd have to do the check on both files first - place the files into respective directories, then use them in the subjob with the tMap. The question I'd have - if you have a lot of main and lookup files, how do you coordinate the lookups between pairs of files? Or do you have only 1 lookup file? In which case you can reference the file in the directory that holds the file that passed your test above...
Hope this helps...
Yes, that's what I was describing... Would that work for you?