[DO NOT MERGE] [TSPS-899] Update Glimpse docker images by salonishah11 · Pull Request #1823 · broadinstitute/warp

salonishah11 · 2026-04-22T22:33:28Z

Description

Jira: https://broadworkbench.atlassian.net/browse/TSPS-899

This PR updates the docker images for GlimpsePhase, GlimpseLigate and CollectQCMetrics tasks.

GlimpsePhase and GlimpseLigate will now use a docker image generated from warp-tools repo (using build script from palantir-workflows repo that builds Glimpse base image and adds necessary tools on top of it). Related PR - [TSPS-899] Add Glimpse docker build GHA and versioning warp-tools#193
CollectQCMetrics will now use a mirro.gcr.io version of Hail image

There are also some other small wdl changes that were made after we ported the Glimpse wdl to Warp. These are either just small bash related changes or necessary changes to make the wdl work with the new Glimpse docker image.

Testing

Tested the image by updating wdl and running the workflow manually. For GlimpsePhase task CPU was set to 1 and preemptibles were removed to test the outputs are same.

Submission with the new docker image - https://app.terra.bio/#workspaces/allofus-drc-imputation/Imputation_Server_Hydrogen_Dev/submission_history/8b8e0f87-1ddf-448c-a8a1-5c3d5b1cca3a
Submission with the existing docker image - https://app.terra.bio/#workspaces/allofus-drc-imputation/Imputation_Server_Hydrogen_Dev/submission_history/2dc2e352-0d01-4d25-ac22-0110ba7db94c

Verified the contents of bcf outputs for GlimpsePhase task for 1 shard for both submissions were same using these commands

bcftools view -H file1.bcf > file1.body
bcftools view -H file2.bcf > file2.body
diff file1.body file2.body           --> returned nothing

bcftools view file1.bcf -Ov -o file1.vcf
bcftools view file2.bcf -Ov -o file2.vcf
diff <(grep -v "^#" file1.vcf) <(grep -v "^#" file2.vcf)        --> returned nothing

Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.

Did you add inputs, outputs, or tasks to a workflow?
Did you modify, delete or move: file paths, file names, input names, output names, or task names?
If you made a changelog update, did you update the pipeline version number?

github-actions · 2026-04-22T22:33:36Z

Remember to squash merge!

github-actions · 2026-04-22T22:33:46Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-22T22:33:48Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-23T18:53:41Z

Remember to squash merge!

github-actions · 2026-04-23T18:53:52Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-23T18:53:52Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-24T19:25:31Z

Remember to squash merge!

github-actions · 2026-04-24T19:25:47Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-24T19:28:11Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-27T21:35:33Z

Remember to squash merge!

github-actions · 2026-04-27T21:35:44Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-27T21:35:46Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-27T22:25:20Z

Remember to squash merge!

github-actions · 2026-04-27T22:25:31Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-27T22:25:33Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-28T13:53:37Z

Remember to squash merge!

github-actions · 2026-04-28T13:53:48Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-28T13:53:49Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-28T19:04:14Z

Remember to squash merge!

github-actions · 2026-04-28T19:04:27Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-28T19:04:31Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-29T17:53:43Z

Remember to squash merge!

github-actions · 2026-04-29T17:53:55Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-29T17:53:56Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-29T20:15:39Z

Remember to squash merge!

github-actions · 2026-04-29T20:15:48Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-04-29T20:15:53Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-30T13:58:44Z

Remember to squash merge!

github-actions · 2026-04-30T13:58:57Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-04-30T14:02:04Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

salonishah11 · 2026-04-30T14:05:12Z


        String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
-        String glimpse_docker = "us.gcr.io/broad-dsde-methods/glimpse:kachulis_ck_bam_reader_retry_cf5822c"
+        String glimpse_docker = "us.gcr.io/broad-gotc-prod/imputation-glimpse:sps_glimpse_docker"


I will update this once warp-tools PR is merged and replace it with the new official image

salonishah11 · 2026-04-30T14:05:31Z

        set -euo pipefail

-        export GCS_OAUTH_TOKEN=$(/root/google-cloud-sdk/bin/gcloud auth application-default print-access-token)
+        export GCS_OAUTH_TOKEN=$(/google-cloud-sdk/bin/gcloud auth application-default print-access-token)


This change is needed to make the wdl work with the new Glimpse docker image

…nstitute/warp into sps_glimpse_docker_images

github-actions · 2026-04-30T14:54:23Z

Remember to squash merge!

github-actions · 2026-04-30T14:54:34Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2026-04-30T14:54:41Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

salonishah11 · 2026-04-30T14:54:47Z

-        cpu: cpu
-        preemptible: preemptible


This will be reverted after testing

github-actions · 2026-05-01T20:49:35Z

Remember to squash merge!

github-actions · 2026-05-01T20:49:45Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-05-01T20:49:52Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2026-05-03T23:39:18Z

Remember to squash merge!

github-actions · 2026-05-03T23:39:30Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-05-03T23:39:31Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

update to test glimpse images

4a1f672

salonishah11 added the DO NOT MERGE label Apr 22, 2026

use docker with gcloud installed

b0d5c2c

build extension on top of glimpse base; modified docker files with fixes

97a2817

use custom docker file - glimpse base + extension

c4bdf05

use different way to install gcloud

7dac613

use gcloud tarball installation approach

1a54144

use palantir's build script but with platform flag

8d78c5b

change gcloud path in wdl to accomodate dockerfile changes

eb857e0

remove preemptible, cpu is 1

9313865

use existing docker image

84b7e77

salonishah11 mentioned this pull request Apr 30, 2026

[TSPS-899] Add Glimpse docker build GHA and versioning broadinstitute/warp-tools#193

Open

cleanup; update changelog

ef2b97f

Updated pipeline_versions.txt with all pipeline version information

3dc1697

salonishah11 commented Apr 30, 2026

View reviewed changes

salonishah11 added 2 commits April 30, 2026 10:53

testing on pumas_50; GlimpsePhase 1 cpu no preemptibles

59fca1c

Merge branch 'sps_glimpse_docker_images' of https://github.com/broadi…

4d2ea17

…nstitute/warp into sps_glimpse_docker_images

salonishah11 commented Apr 30, 2026

View reviewed changes

sps_2024_glimpse_docker image

26cbfed

only essential changes

9f272ae

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salonishah11 commented Apr 22, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Description

Testing

Checklist

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salonishah11 commented Apr 22, 2026 •

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