[Internal] [Bug] Update general_utility.py

[jessicarowell]

There is a fair amount of legacy code in this script (i.e., related to entrypoints). It needs an update. We may not even need it at all anymore.

Run environment (container, cloud service, HPC, platform, etc.)
All

Command to replicate the error:
N/A

Any Additional Context or Information?

[jessicarowell]

Also dig into and possibly remove these which are currently commented out in ./workflows/tostadas.nf

// include { CHECK_FILES } from "../modules/local/general_util/check_files/main"
// include { RUN_UTILITY } from "../subworkflows/local/utility"

[RamiyapriyaS]

Potentially remove "processed_samples" parameter.