Unicyler refactoring kao Clade I Rewrite

[kyleoconnell]

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[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @kyleoconnell,

It looks like this pull-request is has been made against the CDCgov/polkapox master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the CDCgov/polkapox dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[kyleoconnell-CDC]

@mikeyweigand I will send the testing commands offline.