Issue reported by Fengchao:

Percolator stops running when the pin file only has the header: Nesvilab/FragPipe#1426 (comment)

I understand that it is not very meaningful to run Percolator in this case. However, FragPipe does not know that the pin file only has the header during the process. We hope the individual tools will generate header-only output and continue the process. Could you please take a look and (hopefully) make Percolator generate the head-only output tsv files?