If you know the 2 files from the beginning you can simply have a pipeline with 2 entry (fileIO)
I don't know your language, but by design you can do this
PCollection1 PCollection2
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FileIO(readFile1) FileIO(readFile2)
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Transform file Transform file
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WriteIO(sink) WriteIO(sink)
You can imagine side input, flatten, group by,... all depends on your needs.
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