update GATK and fix Freebayes-Mutect2 channels issue

[maxulysse]

nf-core/sarek pull request

Close and fix #200 #209 #210

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[maxulysse]

Tested on our cluster, and the Freebayes Mutect2 channel collision is now gone.
I think it was introduced when @szilvajuhos and I updated Mutect2 with the PON and the filtering.
Sorry all for the inconvenience.

And thanks to @jfnavarro for founding this bug in the first place.

I know it's bad practices, and I should have addressed that in separate PRs, but I also fixed the two issues recently raised by @FriederikeHanssen

So thanks a lot for finding out about that as well.