Implemented TMB score calculation

[bounlu]

Implements #495 based on pyTMB.py starting from draft by @FriederikeHanssen

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[nf-core-bot]

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[FriederikeHanssen]

Amazing 🌟 Looks like this PR also contains the MSISENSOR changes? @Patricie34 is also implementing variant normalisation over in #1682 , can these efforts be combined/ is that implementation something you can build on?

[bounlu]

Yes somehow msisensorpro tumor-only changes also got into this PR and I cannot separate them. I am not sure if I can help with the variant normalization.

[Patricie34]

Yes somehow msisensorpro tumor-only changes also got into this PR and I cannot separate them. I am not sure if I can help with the variant normalization.

Hi, are you planning to finish this PR? I am almost done with the normalization and since I will need to calculate TMB in near future, it would be great to have it implemented in Sarek!
If you agree I would like to join/help with it.

[bounlu]

Hi. It's already finished on my end. I am using it on my version of sarek and it works fine. Please feel free to modify it to integrate to the current version of the public version.

[Patricie34]

Hi. It's already finished on my end. I am using it on my version of sarek and it works fine. Please feel free to modify it to integrate to the current version of the public version.

Oh, I see. So you're not planning to resolve the conflicts here so it could be merged? If it works, I could try to finish it here.

[bounlu]

Hi. It's already finished on my end. I am using it on my version of sarek and it works fine. Please feel free to modify it to integrate to the current version of the public version.

Oh, I see. So you're not planning to resolve the conflicts here so it could be merged? If it works, I could try to finish it here.

done.