Update gatk4 mutect2 to add --alleles parameter for force calling

[jchchiu]

PR checklist

Closes #9019

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For Issue #9019 and nf-core/sarek#1952

[maxulysse]

Nice work

[maxulysse]

how about we rename and reorder these inputs (just to keep a logic with the args from mutect2 and the names?

    path alleles
    path alleles_tbi
    path germline_resource
    path germline_resource_tbi
    path panel_of_normals
    path panel_of_normals_tbi

[maxulysse]

Reorder, because I like a list nicely ordered 😆