Refactor variant calling

[maxulysse]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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[maxulysse]

Issues with the CI was due to some remnants of suffix syntax.
I'm happy with merging at this state, and I'll make more PR(s) for the rest of the VC/Annotation

[maxulysse]

So just need to take care of Freebayes tests.
But I think this might a a bigger issue, so let's do this in another issue

[FriederikeHanssen]

🤩

[github-actions]

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