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Rename "metadata" table to "sample_info" table, fix vet schema #7196

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merged 9 commits into from
Apr 10, 2021

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mmorgantaylor
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@mmorgantaylor mmorgantaylor commented Apr 9, 2021

specops issue #265 https://github.com/broadinstitute/dsp-spec-ops/issues/265

in addition to renaming the metadata table (in both CreateVariantIngestFiles tool and ImportGenomes wdl), this PR:

  • removes interval_list_blob from the metadata/sample_info table
  • adds missing QUALapprox field to the vet schema defaults (in ImportGenomes wdl)

this was tested by running ImportGenomes.wdl in Terra and the sample_info table gets created & populated as expected.

note: ImportArrays.wdl and array tooling were not updated

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@kcibul kcibul left a comment

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Looks great, very thorough. I'm assuming it runs :D

One other place to look through would be example .sh files or .md where we have command lines.

@RoriCremer
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dont we also need to update
scripts/variantstore/wdl/extract/run_gvs_tieout_extract.sh ?
might be worth rebasing to make sure you have Kris' latest changes to that script

@mmorgantaylor mmorgantaylor changed the title Rename "metadata" table to "sample_info" table Rename "metadata" table to "sample_info" table, fix vet schema Apr 9, 2021
@mmorgantaylor mmorgantaylor merged commit 3a2cb47 into ah_var_store Apr 10, 2021
@mmorgantaylor mmorgantaylor deleted the mmt_rename_metadata branch April 10, 2021 16:15
This was referenced Mar 17, 2023
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3 participants