We've got this peristaltic pump for water sampling, it hooks up through a cigarette light (male end) into a female receptacle that has alligator clamps to hook onto a 12V battery.

Is there any reason, we can't bypass the cigarette lighter and have it directly wired to the batter alligator clamps?

Those male 12v plugs have a fuse in them. Just make sure you haven't completely removed the fusing from the circuit and there shouldn't be any reason not to do that.

In most situations that receptacle is fused as well. So you're potentially bypassing 2 fuses.

This is my thought, my co-worker is going to take apart the male cigarette lighter end and see if there is in fact a fuse in there. If there is, I assume we can just wire in a fuse to the new wiring?

No issue at all. Just put a disconnect switch on it so you can turn the pump off and on without any issue. I'd use SAE style connections.

Battery to switch:

[url=https://www.amazon.com/Battery-Tender-081-0069-6-Terminal-Disconnect/dp/B000NCOKZQ/ref=sr_1_1_sspa?crid=3AJF264HKQBNL&dib=eyJ2IjoiMSJ9.mtJeNrOS2xr2PX91PRK5Ai_MfdR_lnCoMfybwrt59Au7UYD7TkujcU_E9OOjGzxj7ajje0nZ97Mcy2cHVzbcUz5zIx4iKoowoel4FX8boQZqMJP8qGXIgOTPOw92dqR6iadArgYUU0IEidIGpuYKzOdTQfK-mWi7fEoQWK5v3vy1x-MnSk07_tYG9aABuOXonv3_5Q9XcUZHT4GGGSEP4frqLOW4bh7JIKdSAVQM6xo.eQltsWhV_vG4yhOSIy1Mhgga3qWypgSs11a2c4mayzU&dib_tag=se&keywords=SAE%2Bconnector%2Bto%2Bbattery&qid=1757096626&sprefix=sae%2Bconnector%2Bto%2Bbattery%2Caps%2C130&sr=8-1-spons&sp_csd=d2lkZ2V0TmFtZT1zcF9hdGY&th=1][/url]SAE to Ring Terminal Connector

SAE Switch:

SAE On/Off Switch

SAE Switch to Pump:

SAE Wire

Confirmed with the manufacturer that there is supposed to be a 10amp fuse in it.

https://www.easternmarine.com/handiman-fuse-holder-180314?gad_source=1&gad_campaignid=20890606536&gbraid=0AAAAAD_k138YmkInAAJgEVrXRbnwnCFr5&gclid=CjwKCAjwlOrFBhBaEiwAw4bYDYUpmlflz8RjZOYvWuD0kqoJWEZ1GXFrudxl6z3a7ccSCxD8aGAHZBoCt6YQAvD_BwE

Gonna just drop one of these into the positive wiring connection.