subprocess

Try refactoring your code like this:

In scan.py, move all the module level code into a function e.g. like:

def run(repo, cpuid):
    # do whatever scan.py does given a repo path and cpuid
    # instead of printing to stdout, have this return a value

If you still care about scan.py having a command-line interface as well, add:

import argparse

def main(argv=None):
    parser = argparse.ArgumentParser()
    # ... implement command-line argument parsing here
    args = parser.parse_args(argv)
    value = run(args.repo, args.cpuid)
    print(value)

if __name__ == '__main__':
    main()

Now in your run.py do something like:

import multiprocessing
import scan  # maybe give this a more specialized name

def work(args):
    repo, cpuid = args
    output = scan.run(repo, cpuid)
    for line in output.splitlines():
         # Do whatever you want to do here...

def main():
    repos = ... # You didn't show us where this comes from
    pool = multiprocessing.Pool()  # Or pass however many processes
    pool.map(work, [(r[0], '1-240') for r in repos])

if __name__ == '__main__':
    main()

Something like this. The point I'm trying to make here is that if you factor your code wisely it will make multiprocessing much simpler. Some of the details here are slightly opinionated, however.