paul j3 <ajipa...@gmail.com> added the comment:

Put the required positional first

$ myapp myfile -s

or one of the store_true arguments

$ myapp -s -j myfile

I think

$ myapp -s -- myfile

will work as well, but that needs to be tested.  

The '-s' has to be followed by something won't be confused for an argument, 
such as nothing, or a flag.

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Python tracker <rep...@bugs.python.org>
<https://bugs.python.org/issue45673>
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