This application can be used through the GUI or via the command line. (CLI)

Command line usage:
qstlink2 [-hqvcwreV] [path]

-h, --help: shows this help
-q, --quiet: Quiet output (Nothing)
-v, --verbose: Verbose output (Debug)
-c,--cli: Enable command line mode
-w,--write: Enable write mode - Needs Path
-r,--read: Enable read mode - Needs Path
-e,--erase: Flash will be completely erased
-V, --verify: When used with write, the file will be verified against flash
-R, --reset: will reset the MCU

Example to write and verify the device:
qstlink2 -cwV /home/me/myfile.bin (you can also use relative paths like ./test.bin)
or
qstlink2 --cli --write --verify /home/me/myfile.bin

More info here