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[DRAFT] Beagle Imputation WDL#1238

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mmorgantaylor wants to merge 26 commits intodevelopbroadinstitute/warp:developfrom TSPS-175_mma_beagle_imputationbroadinstitute/warp:TSPS-175_mma_beagle_imputationCopy head branch name to clipboard

+518-2

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Commits on Feb 7, 2024

• Merge pull request #1198 from broadinstitute/staging

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  nikellepetrillo

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  9f137a7

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• Merge pull request #1200 from broadinstitute/develop

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  nikellepetrillo

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Commits on Feb 8, 2024

• Merge pull request #1202 from broadinstitute/staging

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  nikellepetrillo

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Commits on Feb 16, 2024

• Merge pull request #1208 from broadinstitute/develop

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  nikellepetrillo

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Commits on Feb 20, 2024

• Merge pull request #1209 from broadinstitute/staging

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  nikellepetrillo

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  b8a32c7

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Commits on Feb 28, 2024

• wip add beagle imputation stuff

  mmorgantaylor

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  c65dc53

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• add 2 wdls to dockstore.yml

  mmorgantaylor

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  2306187

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• fix docker gar url

  mmorgantaylor

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  85e19de

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• use the right path for jars

  mmorgantaylor

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  7e2be90

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• wip on imputation wdl

  mmorgantaylor

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  9c64eeb

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• oops use correct jar

  mmorgantaylor

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  39482c4

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• missing equals

  mmorgantaylor

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  f175179

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• fix java call again

  mmorgantaylor

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  648f938

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Commits on Feb 29, 2024

• fix java call

  mmorgantaylor

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  14357bf

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• oops match file names

  mmorgantaylor

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Commits on Mar 1, 2024

• update beagle jar to 01Mar24.d36

  mmorgantaylor

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Commits on Mar 2, 2024

• debug GatherVcfs

  mmorgantaylor

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  435ba19

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• debug GatherVcfs 2

  mmorgantaylor

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  b72281a

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• try to resolve missing file issue

  mmorgantaylor

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  fd04907

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Commits on Mar 4, 2024

• don't impute over padding

  mmorgantaylor

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  bce4c9d

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• make the index again

  mmorgantaylor

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  64d307f

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Commits on Mar 8, 2024

• supply vcf_index input to SelectVariantsByIds

  mmorgantaylor

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  54b05d6

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Commits on Mar 15, 2024

• update Imputation wdl too

  mmorgantaylor

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  f2efe2c

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• newlines

  mmorgantaylor

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  0d3c862

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Commits on Mar 19, 2024

• update for hg38

  mmorgantaylor

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  3757137

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• Revert "update for hg38"

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  mmorgantaylor

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