Wabbajack is an amazing program for windows. But most people don't know that there's an unofficial port of it for Linux! I have multiple full wabbajack modlists set up, hundreds upon hundreds of GBs. Not a single issue, at least, none that I wouldn't have also faced on windows (i.e. Bethesda quirks). Works best with the native Steam version (sudo apt install steam, use sudo dpkg --add-architecture i386 to install it cleanly with NVIDIA GPUs). Jackify creates an integrated shortcut to Mod Organizer 2 that links seamlessly to the game you're modding. Best part is, if you have multiple SSDs, you can recreate the shortcut in Steam even after distro hopping. I've been using the same custom modded Skyrim install from Arch to Ubuntu to here. Here's the link for anyone interested. 
Does this only work with the games that is listed on Github for Wabbajack ???? ....
I believe so, but there may be a way around it. You can theoretically install a very minimal modlist (Halgari's Helper for Skyrim is less than 1 GB) for any game. It would take some tweaking past that point, but it would create a Mod Organizer shortcut for any game, in theory. I haven't tried, lol
I use Nexus for mods in The Hunter Call Of The Wild ..... here is an example of a mod installation for COTW ..... very easy to use on Steam .... you can find more info on YouTube or your search engine .....
Sorry I deleted the instruction before someone flags my post for something they feel might be illegal and it gets deleted anyway ....
I should note I only use these for my personal enjoyment and I never play any game in multiplayer ..... or in competitions ..... single player only ....
I didn't see yours but I have some highly inappropriate mods in almost every modlist lol, no judgement here,