SFTP is actually a full featured remote file system protocol. Using it, it would be posible to process the data without downloading it first to the local harddisk. You could even write the output file directly on the remote host so sensible data never gets stored on your system.

Net::SFTP or Net::SFTP::Foreign would allow you to do so.

For maximun security, ssh keys should be protected by a keyphrase, but that would require to launch the process manually.