Am I correct to include a comma before "but instead" in the following example? I am not sure if the latter part of the sentence could be considered a main clause because there is no subject, so I am not sure if I am right or not.
The manual holds that women must not choose a programme themselves, but instead wait to be assigned to a module.
The manual holds that women mustn't choose a programme themselves, but instead wait to be assigned to a module.
You use a comma before "but" if it introduces an independent complete clause.
As there's no independent clause after "but" in the sentence presented above, it doesn't need a comma before "but".
The manual holds that women must not choose a programme themselves, but instead wait to be assigned to a module.
Comma usage varies among writers. Unless you are supposed to be writing according to the dictates of a certain style guide, then you should include a comma only if greatly helps the reader. I don't think it greatly helps the reader here and so it can be omitted.
People generally overuse commas, so it's always a good exercise to read through what one has written and eliminate any unnecessary ones.
Consider:
When I write or teach I am also very much against the overuse of commas.
Which is one reason I wrote the preceding sentence with no comma, although by "rules of comma usage" one or two could have been included and not considered a grammatical error.
One place they usually do not help the reader is when they come between a subject and a verb, as in
The local sheriff, rounded up the bad guys.
It is useful, however, to use one here:
The local sheriff, whose name was Clint, rounded up the bad guys.
