I had a few single FLAC files with cue files I wanted to put into Plex but to my dismay it doesn’t read the CUE files at all. Thus I needed to split the one FLAC file into multiple pieces with shnsplit. Thanks to Stack Exchange for the help.

On my Debian system:

 sudo apt install cuetools shntool flac

With the necessary tools installed you simply have to run the shnsplit command:

 shnsplit -f FILENAME.cue -t "%a - %n %t - %p" FILENAME.flac

the -t parameters formats the filename as desired per the manpage

-t fmt
Name output files in user‐specified format based on CUE sheet fields. The following formatting strings are recognized: 

%p
Performer
%a
Album
%t
Track title
%n
Track number