TSPS-241 Clean up beagle wdl

[jsotobroad]

Description

wanted to do a clean up a few things in this pr

• Remove extra QC steps task (and optional input etc)

• Remove option to split output to single sample

• Remove chunks_fail_threshold input; Consult with Brian about failing chunks if not enough variant overlap with ref panel

  • if a chunk fails this check, don't impute and fail the workflow

Example of workflow that had an failing chunk - https://bvdp-saturn-dev.appspot.com/#workspaces/tsps_dev_bp_02_01_2024_v1/imputation-pipeline-testing-03-07-2024/workflows-app/submission-monitoring/c0baf9cb-2d4d-4e25-851d-35a0f702d1ba/c49799aa-2891-498e-b438-724e2d6216cb

Example of successful workflow -https://bvdp-saturn-dev.appspot.com/#workspaces/tsps_dev_bp_02_01_2024_v1/imputation-pipeline-testing-03-07-2024/workflows-app/submission-monitoring/da4b13ed-5ee1-469e-b6f2-e65783e92e05/5039155f-5dae-4912-a5f6-69bf9d30df4a

vcf checker workflow to verify the outputs are the same - https://bvdp-saturn-dev.appspot.com/#workspaces/tsps_dev_bp_02_01_2024_v1/imputation-pipeline-testing-03-07-2024/workflows-app/submission-history/13d5e128-a205-4ff0-a76f-e7bd749022b0

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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?