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Allow missing age values in mt merge pipeline#1785

Merged
jessicaway merged 3 commits intodevelopfrom
jw_patch_mt_merge
Feb 26, 2026
Merged

Allow missing age values in mt merge pipeline#1785
jessicaway merged 3 commits intodevelopfrom
jw_patch_mt_merge

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Description

Give your PR a concise yet descriptive title.
Please explain the changes you made here.
Explain the motivation for making this change. What existing problem does the pull request solve?
Mention any issues fixed, addressed, or otherwise related to this pull request, including issue numbers or hard links for issues in other repos.
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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?

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Remember to squash merge!

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🔍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.

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🔍Changelog Validation Results:

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

Comment thread all_of_us/mitochondria/mt_coverage_merge.wdl

runtime {
docker: "us.gcr.io/broad-gotc-prod/aou-mitochondrial-combine-vcfs-covdb:1.0.0"
docker: "us.gcr.io/broad-gotc-prod/aou-mitochondrial-combine-vcfs-covdb:1.0.1"
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are these docker indents off?

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@ekiernan ekiernan left a comment

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Approve, but would like to see a test run of the code with problematic samples before we kick off 500K

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Remember to squash merge!

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🔍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
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🔍Changelog Validation Results:

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

@jessicaway
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Here is a pipeline run with problematic samples and the most recent version of the code (fixing the docker indent): https://app.terra.bio/#workspaces/allofus-drc-prod-auxiliary/Mitochondria_AoU_Workspace/submission_history/46f8dbb0-8d27-4710-ad5e-548f09fa61c0

@jessicaway jessicaway merged commit 119bc8f into develop Feb 26, 2026
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@jessicaway jessicaway deleted the jw_patch_mt_merge branch February 26, 2026 14:59
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3 participants