Add -o option to unzip calls

[brynpickering]

Fixes #327

Checklist

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• CHANGELOG updated
• Minimal workflow tests pass
• Tests added to cover contribution
• Documentation updated
• Configuration schema updated

[timtroendle]

I see how this is solving the issue #327. I would still be reluctant to merge this, because #327 should never happen. Snakemake should take care that the file to be generated is deleted before executing the rule.

I recommend to first better understand #327. Can we reproduce it? Maybe it's a bug in Snakemake? Maybe that bug is solved already in some newer version? Maybe we can solve the bug ourselves?

[brynpickering]

It happens for me too. It's because the output is just one of the files that is unzipped, not all of them. I can fix it properly in this instance, but there are other instances in which -o is used.

EDIT: I have now cleaned these up to all be able to unzip without needing -o by only extracting the files that are actually needed.