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Small updates to GVS Integration WDL [VS-618] #8042

Merged
merged 5 commits into from
Sep 29, 2022
Merged

Small updates to GVS Integration WDL [VS-618] #8042

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5ce8194
what if we just use FORTY
rsasch Sep 27, 2022
dc27c2f
Merge branch 'ah_var_store' into rsa_vs_618_integration
rsasch Sep 28, 2022
0aab21b
Merge branch 'ah_var_store' into rsa_vs_618_integration
rsasch Sep 28, 2022
f12caa6
turned off xtrace where it made the logs hard to read, updated docker…
rsasch Sep 28, 2022
c21643d
dockstore
rsasch Sep 29, 2022
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1 change: 1 addition & 0 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -208,6 +208,7 @@ workflows:
branches:
- master
- ah_var_store
- rsa_vs_618_integration
- name: GvsIngestTieout
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
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13 changes: 5 additions & 8 deletions scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
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Expand Up @@ -49,7 +49,7 @@ workflow GvsQuickstartIntegration {
]

Int? extract_scatter_count
String drop_state = "NONE"
String drop_state = "FORTY"
}
String project_id = "gvs-internal"

Expand Down Expand Up @@ -119,7 +119,6 @@ task AssertIdenticalOutputs {
set -o errexit
set -o nounset
set -o pipefail
set -o xtrace
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😿

I'd be sad to see these xtraces wiped out as they have saved my bacon many times. Happy to discuss this at (post) standup tomorrow.


failures=()

Expand Down Expand Up @@ -190,7 +189,7 @@ task AssertIdenticalOutputs {
>>>

runtime {
docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:398.0.0"
docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
disks: "local-disk 500 HDD"
}

Expand All @@ -217,7 +216,6 @@ task AssertCostIsTrackedAndExpected {
set -o errexit
set -o nounset
set -o pipefail
set -o xtrace

echo "project_id = ~{project_id}" > ~/.bigqueryrc
bq query --location=US --project_id=~{project_id} --format=csv --use_legacy_sql=false \
Expand Down Expand Up @@ -288,7 +286,7 @@ task AssertCostIsTrackedAndExpected {
>>>

runtime {
docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:398.0.0"
docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
disks: "local-disk 10 HDD"
}

Expand All @@ -314,7 +312,6 @@ task AssertTableSizesAreExpected {
set -o errexit
set -o nounset
set -o pipefail
set -o xtrace

echo "project_id = ~{project_id}" > ~/.bigqueryrc
bq query --location=US --project_id=~{project_id} --format=csv --use_legacy_sql=false \
Expand All @@ -323,7 +320,7 @@ task AssertTableSizesAreExpected {
UNION ALL \
SELECT 'ref_ranges_total' AS total_name, sum(total_billable_bytes) AS total_bytes \
FROM \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` \
WHERE table_name LIKE 'ref_ranges_%'" > table_size_output.csv
WHERE table_name LIKE 'ref_ranges_%' ORDER BY total_name" > table_size_output.csv

set +o errexit
diff -w table_size_output.csv ~{expected_output_csv} > differences.txt
Expand All @@ -337,7 +334,7 @@ task AssertTableSizesAreExpected {
>>>

runtime {
docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:398.0.0"
docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
disks: "local-disk 10 HDD"
}

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