TSPS-221 remove index input and add seed to make beagle tool deterministic

[jsotobroad]

Description

We want to remove the input vcf index and just create the index as part of a task. We want to make the beagle tool deterministic so we provide a value for nthreads and seed

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Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.

• [ ] Did you add inputs, outputs, or tasks to a workflow?
• [ ] Did you modify, delete or move: file paths, file names, input names, output names, or task names?
• [ ] If you made a changelog update, did you update the pipeline version number?

[dsde-jenkins]

Can one of the admins verify this patch?