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GvsUnified WDL to wrap the 6 core GVS WDLs [VS-382] #7789

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merged 3 commits into from
Apr 21, 2022

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mcovarr
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@mcovarr mcovarr commented Apr 15, 2022

tl;dr This isn't the full ask for VS-357 but being able to run the Quickstart by launching 1 WDL instead 6 may represent a useful increment of work.

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Looks good so far!

# Begin GvsPrepareRangesCallset
String extract_table_prefix

String query_project = project_id
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Duplicate with that on line 56.
And why is this even needed?

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@mcovarr mcovarr Apr 15, 2022

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Good catch! I'm surprised WDL allows completely duplicate declarations like that 😦

The query and destination versions of project and dataset are used in GvsPrepareCallset and GvsExtractCallset, though I do not know circumstances under which they would be used.

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They are used with GvsExtractCohortFromSampleNames.wdl where the GVS dataset and the delivered/billed datasets might be different.

String extract_table_prefix

String query_project = project_id
String destination_project = project_id
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Why is destination_project needed?

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They are used with GvsExtractCohortFromSampleNames.wdl where the GVS dataset and the delivered/billed datasets might be different.

@mcovarr mcovarr force-pushed the vs_357_integration branch 2 times, most recently from a4c56ae to 0c43bf2 Compare April 15, 2022 20:36
@mcovarr mcovarr changed the title GvsUnified WDL to wrap the 6 Quickstart workflows [VS-357] GvsUnified WDL to wrap the 6 Quickstart workflows [VS-382] Apr 19, 2022
@mcovarr mcovarr changed the title GvsUnified WDL to wrap the 6 Quickstart workflows [VS-382] GvsUnified WDL to wrap the 6 core GVS workflows [VS-382] Apr 19, 2022
@mcovarr mcovarr changed the title GvsUnified WDL to wrap the 6 core GVS workflows [VS-382] GvsUnified WDL to wrap the 6 core GVS WDLs [VS-382] Apr 19, 2022
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Travis reported job failures from build 38974
Failures in the following jobs:

Test Type JDK Job ID Logs
conda openjdk8 38974.5 logs

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Travis reported job failures from build 38980
Failures in the following jobs:

Test Type JDK Job ID Logs
conda openjdk8 38980.5 logs

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Travis reported job failures from build 38995
Failures in the following jobs:

Test Type JDK Job ID Logs
conda openjdk8 38995.5 logs

@mcovarr mcovarr merged commit 8f429ad into ah_var_store Apr 21, 2022
@mcovarr mcovarr deleted the vs_357_integration branch April 21, 2022 14:11
This was referenced Mar 17, 2023
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4 participants