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SA support and consistent naming for all GVS WDLs #7205

Merged
merged 38 commits into from
Apr 16, 2021
Merged

SA support and consistent naming for all GVS WDLs #7205

merged 38 commits into from
Apr 16, 2021

Commits on Apr 15, 2021

  1. rename ngs_filter_extract.wdl -> GvsCreateFilterSet.wdl

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  2. add branch to dockstore, first pass at SA auth in GvsCreateFilterSet

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    mmorgantaylor committed Apr 15, 2021
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  3. rename ngs_cohort_extract.wdl -> GvsExtractCallset.wdl

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  4. add defaults to GvsCreateFilterSet tranche and annotation values inputs

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  5. try export GOOGLE_APPLICATION_CREDENTIALS='~{service_account_json}'

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  6. reformat without quotes

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  7. remove extra SA json input to task

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  8. pass SA to BQ upload task

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  9. specify project for ExtractFilterTask

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  10. put project setting in the correct task

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  11. add project setting to ExtractFilterTask

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  12. add projectID to getQueryCostBytesProcessedEstimate

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    mmorgantaylor committed Apr 15, 2021
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  13. first pass at add SA support to GvsExtractCallset

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  14. fix output file for ExtractFeatures

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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  15. add freq_table function inline

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    mmorgantaylor committed Apr 15, 2021
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  16. testing - add cat bigqueryrc file to CreateTables

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    mmorgantaylor committed Apr 15, 2021
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  17. add branch to dockstore for ImportGenomes

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    mmorgantaylor committed Apr 15, 2021
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  18. remove cat bigqueryrc

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    mmorgantaylor committed Apr 15, 2021
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  19. add --quiet flag to bq load command

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    mmorgantaylor committed Apr 15, 2021
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  20. try taking last line of bq load output

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    mmorgantaylor committed Apr 15, 2021
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  21. add parens to feature_extract.sql expression

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    mmorgantaylor committed Apr 15, 2021
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  22. grab last line actually well

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    mmorgantaylor committed Apr 15, 2021
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  23. add projectID to query generation

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    mmorgantaylor committed Apr 15, 2021
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  24. refactor ImportGenomes -> GvsImportGenomes.wdl

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    mmorgantaylor committed Apr 15, 2021
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  25. update example inputs for GvsImportGenomes

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    mmorgantaylor committed Apr 15, 2021
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  26. add projectID to executeQuery

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    mmorgantaylor committed Apr 15, 2021
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  27. add unit test for query with project method

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    mmorgantaylor committed Apr 15, 2021
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  28. add example.inputs.json for wdls

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    mmorgantaylor committed Apr 15, 2021
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  29. update prepare callset example inputs

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    mmorgantaylor committed Apr 15, 2021
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  30. add UDFs (freq_table) to query generation

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    mmorgantaylor committed Apr 15, 2021
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  31. working UDFs

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    mmorgantaylor committed Apr 15, 2021
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  32. add fresh jar to wdl example inputs

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    mmorgantaylor committed Apr 15, 2021
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  33. remove unneeded inputs file, add WDL Testing readme

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    mmorgantaylor committed Apr 15, 2021
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  34. add null udfs to fix unit tests

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    mmorgantaylor committed Apr 15, 2021
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  35. fix ternery logic

    @mmorgantaylor
    mmorgantaylor committed Apr 15, 2021
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Commits on Apr 16, 2021

  1. consistent SA authing

    @mmorgantaylor
    mmorgantaylor committed Apr 16, 2021
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  2. do gsutil mv for set files

    @mmorgantaylor
    mmorgantaylor committed Apr 16, 2021
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  3. fix bad project value

    @mmorgantaylor
    mmorgantaylor committed Apr 16, 2021
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