Flags

      while (<INFILE>) {
        ...
        $chain_test=1  if (/CHAIN_TEST/);

        if (/apply/ && ($chain_test)) {
          ...
        }
      }

It's still valuable to avoid such flag variables if possible
Their state is one more thing to remember while debugging
Sometimes there is a way that is just as simple with no flag

      while (<INFILE>) {  last if /CHAIN_TEST/ }

      while (<INFILE>) {
        ...
        if (/apply/) {
          ...
        }
      }