Logstash Pipeline Fails (LF/CR)

When processing log files that end with a line feed/carriage return, the pipeline is unable to process the file. The work around is to open the file in some sort of text editor (Notepad++) and manually backspace the resulting blank line and saving the file. Then logstash immediately will process the log.

Is there a better way to process these files, the manual work around is tedious on large numbers of log files. "sed" also seemed ineffective, the notepad++ manual removal is the only way I've been able to figure out how to get these logs to process.

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Another work around is to:
truncate -s -1

These are workarounds, though, seems like logstash should be able to handle a standard text log file (which normally terminates with a 0x0a)