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Update the GATK base image to a newer LTS ubuntu release #8610

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merged 13 commits into from
Dec 12, 2023

Restore epsilon, switch to release base image, update scripts and docs

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Merged

Update the GATK base image to a newer LTS ubuntu release #8610

Restore epsilon, switch to release base image, update scripts and docs
92ce8ac
Select commit
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Codecov / codecov/patch succeeded Dec 12, 2023 in 0s

20.455% of diff hit (target 86.401%)

View this Pull Request on Codecov

20.455% of diff hit (target 86.401%)

Annotations

Check warning on line 163 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ExtractVariantAnnotationsIntegrationTest.java

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@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ExtractVariantAnnotationsIntegrationTest.java#L161-L163 

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Check warning on line 167 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ExtractVariantAnnotationsIntegrationTest.java

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@codecov codecov / codecov/patch

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Check warning on line 172 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ExtractVariantAnnotationsIntegrationTest.java

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@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ExtractVariantAnnotationsIntegrationTest.java#L170-L172 

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Check warning on line 169 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java

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@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java#L167-L169 

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Check warning on line 173 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java

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@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java#L171-L173 

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Check warning on line 177 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/ScoreVariantAnnotationsIntegrationTest.java

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@codecov codecov / codecov/patch

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Check warning on line 29 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/SystemCommandUtilsTest.java

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@codecov codecov / codecov/patch

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@codecov codecov / codecov/patch

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@codecov codecov / codecov/patch

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@codecov codecov / codecov/patch

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Check warning on line 185 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java

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@codecov codecov / codecov/patch

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Check warning on line 189 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java

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@codecov codecov / codecov/patch

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Check warning on line 255 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java

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@codecov codecov / codecov/patch

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Check warning on line 259 in src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java

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@codecov codecov / codecov/patch

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/TrainVariantAnnotationsModelIntegrationTest.java#L259 

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