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Removed usage of service account from WDLs
Removed usage of service account from: GvsAssignIds.wdl GvsImportGenomes.wdl GvsCreateAltAllele.wdl GvsCreateFilterSet.wdl GvsWithdrawSamples.wdl GvsCreateAltAllele.wdl GvsPrepareRangesCallset.wdl GvsExtractCallset.wdl GvsExtractCohortFromSampleNames.wdl GvsUnified.wdl GvsJointVariantCalling.wdl GvsAoUReblockGvcf.wdl GvsBenchmarkExtractTask.wdl GvsRescatterCallsetInterval.wdl
In order to test this, I created a small (10 sample) test set using all of us data. That is here Here are successful runs of the following wdls: GvsAssignIds GvsImportGenomes GvsCreateAltAllele GvsCreateFilterSet GvsPrepareRangesCallSet GvsExtractCallSet GvsCreateVAT GvsValidateVAT GvsUnified GvsJointVariantCalling GvsRescatterCallsetInterval - Failed but got beyond the point where it would need the service account. GvsBenchmarkExtractTest - Failed, but got beyond the point where it would need the service account. GvsCallsetCost (unaffected, but tested anyway) GvsAoUReblockGvcf - Tested by Morgan GVSCacluatedPrecisionAndSensitivity (unaffected) GvsJointVariantCallingCallsetCost (unaffected) GvsQuickstartIntegration (unaffected)
Codecov Report
:exclamation: No coverage uploaded for pull request base (
ah_var_store@42a9382
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@@ Coverage Diff @@
## ah_var_store #7985 +/- ##
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Coverage ? 86.243%
Complexity ? 35203
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Files ? 2173
Lines ? 165016
Branches ? 17792
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Hits ? 142315
Misses ? 16376
Partials ? 6325
Confirmed that GvsAoUReblockGvcf.wdl
works 👍