cookiecutter always adds unmatched normal to default config

[rdmorin]

Could the cookiecutter be modified to ask whether the user wants to analyze unpaired tumours with with unmatched normal? I don't think this is asked (or at least not in a way that is intuitive) so I keep ending up with this config.

            genome:
                run_paired_tumours: True
                run_unpaired_tumours_with: "unmatched_normal"
                run_paired_tumours_as_unpaired: False
            capture:
                run_paired_tumours: True
                run_unpaired_tumours_with: "unmatched_normal"
                run_paired_tumours_as_unpaired: False```

[BrunoGrandePhD]

That can definitely be done. In fact, with the new generate_pairs() function, I think the same options should be available for the cookiecutter template, namely matched_only, allow_unmatched, and no_normal (in addition to omit). I can tackle this on the weekend.