I had issues with this a while back, too, until @dos straightened me out: L5 - Deader Than A Doornail After Battery Ran Dry - #44 by dos (You can read a few posts there for more info, which I had forgotten. Sorry. 
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So you could run the command without copying the files over, but after the write_flash.sh part you would need to then add the full path to that tps...bin file, i.e. including the “directory/subdirectory/tps…bin” in full, so that the script would know where it is.
It’s somewhat easier to just copy the needed files into the same folder where you’re running the command.
But if you have the firmware in a separate location:
tree@DB:~/librem5-devkit-tools-pureos-latest$./scripts/write_flash.sh /home/tree/Downloads/firmware-tps6598x-nonfree-master/tps65982-librem5-dp-alt-mode.bin
(If the firmware folder is located in your Downloads directory. Relace with “Desktop” or whatever if it’s somewhere else.)