There are several factors to take into account. One key one is the reliability of whether the external program will be present on all systems where your software is installed. If there is a possibility that it will be missing, then maybe it is better to do it inside your program.
Weighing against that, you might consider that the extra code loaded into your program is prohibitive - you don't need the code bloat for such a seldom-used part of your application.
The system() function is convenient, but dangerous, not least because it invokes a shell, usually. You may be better off calling the program more directly - on Unix, via the fork() and exec() system calls. [Note that a system call is very different from calling the system()
function, incidentally!] OTOH, you may need to worry about ensuring all open file descriptors in your program are closed - especially if your program is some sort of daemon running on behalf of other users; that is less of a problem if your are not using special privileges, but it is still a good idea not to give the invoked program access to anything you did not intend. You may need to look at the fcntl()
system call and the FD_CLOEXEC
flag.
Generally, it is easier to keep control of things if you build the functionality into your program, but it is not a trivial decision.