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Extract Cohort optimizations [VS-493] [VS-1516] #9055

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merged 16 commits into from
Dec 10, 2024
Merged

Extract Cohort optimizations [VS-493] [VS-1516] #9055

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26322e2
wip
mcovarr Nov 23, 2024
01a9bef
more dropping, more logging
mcovarr Nov 23, 2024
399d627
gah
mcovarr Nov 23, 2024
83879b0
Docker
mcovarr Nov 23, 2024
9330c4f
yolo
mcovarr Nov 23, 2024
6eaf6c3
Docker
mcovarr Nov 24, 2024
0f05a8c
Docker
mcovarr Nov 24, 2024
76bd38c
minor fixes, not worth rebuilding Docker
mcovarr Nov 24, 2024
5a8e612
minor updates
mcovarr Nov 25, 2024
f4a945c
Docker
mcovarr Nov 26, 2024
77ce106
begin additional restructuring
mcovarr Nov 26, 2024
bdefb19
cleanup of existing code
mcovarr Nov 27, 2024
4642a58
Docker
mcovarr Nov 27, 2024
6e8bd89
Docker
mcovarr Nov 28, 2024
544db48
windowing comments wip
mcovarr Dec 4, 2024
744ed2a
windowing comments
mcovarr Dec 4, 2024
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4 changes: 3 additions & 1 deletion .dockstore.yml
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Expand Up @@ -173,6 +173,7 @@ workflows:
branches:
- master
- ah_var_store
- vs_1516_yolo
tags:
- /.*/
- name: GvsImportGenomes
Expand Down Expand Up @@ -241,6 +242,7 @@ workflows:
branches:
- master
- ah_var_store
- vs_1516_yolo
tags:
- /.*/
- name: GvsWithdrawSamples
Expand Down Expand Up @@ -314,7 +316,7 @@ workflows:
branches:
- master
- ah_var_store
- vs_1490_fix_curate_input_array_files
- vs_1516_yolo
tags:
- /.*/
- name: GvsIngestTieout
Expand Down
2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsUtils.wdl
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Expand Up @@ -74,7 +74,7 @@ task GetToolVersions {
String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim"
String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2024-11-25-alpine-913039adf8f4"
String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024-11-24-gatkbase-1807487d5912"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024-11-28-gatkbase-b71132a18899"
String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"
String gotc_imputation_docker = "us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.5-1.10.2-0.1.16-1649948623"
String plink_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/plink2:2024-04-23-slim-a0a65f52cc0e"
Expand Down
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