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Support for TDR DRS URIs in Import #7528

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merged 9 commits into from
Nov 2, 2021
Merged

Support for TDR DRS URIs in Import #7528

merged 9 commits into from
Nov 2, 2021

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kcibul
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@kcibul kcibul commented Oct 27, 2021 •
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  • disabled localization optional
  • changed datatype from Array[File] to Array[String]
  • added parameter for indexes (since they can live in different locations)
  • do our own localization in all cases

ahaessly
ahaessly approved these changes Oct 27, 2021
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just one question

scripts/variantstore/wdl/GvsImportGenomes.wdl
fi
# we always do our own localization
gsutil cp $input_vcf .
gsutil cp $input_vcf_index .
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does this mean that we can't run this/test with files on our local filesystem? maybe this isn't a valid use case though.

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@kcibul kcibul Oct 27, 2021 •
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true -- though like you point out we don't really run these WDLs locally (and they need GCS anyway for the bucket to load to bq, etc)

@kcibul kcibul merged commit 08446bb into ah_var_store Nov 2, 2021
@kcibul kcibul deleted the kc_no_streaming branch November 2, 2021 14:23
This was referenced Mar 17, 2023
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@kcibul @ahaessly