An attempt at a project template that works for me (that doesn't necessarily mean you). The proof is (or will hopefully be) in the pudding.
(with cookiecutter available)
cookiecutter --directory bioproject https://github.com/WardDeb/pudding
cookiecutter --directory nfproject https://github.com/WardDeb/pudding
cookiecutter --directory pyproject https://github.com/WardDeb/pudding