gatk docker update 4.6.1.0 #1403

nikellepetrillo · 2024-10-28T17:26:51Z

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?

github-actions · 2024-10-28T17:27:03Z

Remember to squash merge!

github-actions · 2024-10-28T17:27:15Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
CheckFingerprint.wdl has not been changed and needs updating
RNAWithUMIsPipeline.wdl has not been changed and needs updating
AnnotationFiltration.wdl has not had its version updated
UltimaGenomicsWholeGenomeGermline.wdl has not been changed and needs updating
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not had its version updated
JointGenotypingByChromosomePartOne.wdl has not been changed and needs updating
JointGenotypingByChromosomePartTwo.wdl has not been changed and needs updating
ReblockGVCF.wdl has not had its version updated
JointGenotyping.wdl has not had its version updated
UltimaGenomicsJointGenotyping.wdl has not had its version updated
VariantCalling.wdl has not had its version updated
UltimaGenomicsWholeGenomeCramOnly.wdl has not been changed and needs updating
GDCWholeGenomeSomaticSingleSample.wdl has not had its version updated
BroadInternalRNAWithUMIs.wdl has not been changed and needs updating
BroadInternalUltimaGenomics.wdl has not been changed and needs updating
BroadInternalArrays.wdl has not been changed and needs updating
BroadInternalImputation.wdl has not been changed and needs updating
Arrays.wdl has not been changed and needs updating
ValidateChip.wdl has not had its version updated
Imputation.wdl has not been changed and needs updating
IlluminaGenotypingArray.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeReprocessing.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-10-28T17:27:16Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
CheckFingerprint.changelog.md has not been changed and needs to be updated
RNAWithUMIsPipeline.changelog.md has not been changed and needs to be updated
AnnotationFiltration.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeGermline.changelog.md has not been changed and needs to be updated
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartOne.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartTwo.changelog.md has not been changed and needs to be updated
ReblockGVCF.changelog.md has not been changed and needs to be updated
JointGenotyping.changelog.md has not been changed and needs to be updated
UltimaGenomicsJointGenotyping.changelog.md has not been changed and needs to be updated
VariantCalling.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeCramOnly.changelog.md has not been changed and needs to be updated
GDCWholeGenomeSomaticSingleSample.changelog.md has not been changed and needs to be updated
BroadInternalRNAWithUMIs.changelog.md has not been changed and needs to be updated
BroadInternalUltimaGenomics.changelog.md has not been changed and needs to be updated
BroadInternalArrays.changelog.md has not been changed and needs to be updated
BroadInternalImputation.changelog.md has not been changed and needs to be updated
Arrays.changelog.md has not been changed and needs to be updated
ValidateChip.changelog.md has not been changed and needs to be updated
Imputation.changelog.md has not been changed and needs to be updated
IlluminaGenotypingArray.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

nikellepetrillo · 2024-10-28T17:50:06Z

scientific tests running here: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-smart-tests/8662/

pipelines/broad/arrays/validate_chip/ValidateChip.wdl

tasks/broad/BamProcessing.wdl

tasks/broad/CheckContaminationSomatic.wdl

tasks/broad/RNAWithUMIsTasks.wdl

meganshand · 2024-10-28T19:41:27Z

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl

-  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
-  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0"
+  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
+  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0"


Has this version of gatk been uploaded to azurecr.io? I believe Kevin did this for 4.6.0.0, and I'm not sure if we added this to the gatk release process yet or not. I think this was a todo still for the GATK team at the time of the 4.6.0.0 release.

github-actions · 2024-10-28T19:55:33Z

Remember to squash merge!

github-actions · 2024-10-28T19:55:43Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
CheckFingerprint.wdl has not been changed and needs updating
RNAWithUMIsPipeline.wdl has not been changed and needs updating
AnnotationFiltration.wdl has not had its version updated
UltimaGenomicsWholeGenomeGermline.wdl has not been changed and needs updating
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not had its version updated
JointGenotypingByChromosomePartOne.wdl has not been changed and needs updating
JointGenotypingByChromosomePartTwo.wdl has not been changed and needs updating
ReblockGVCF.wdl has not had its version updated
JointGenotyping.wdl has not had its version updated
UltimaGenomicsJointGenotyping.wdl has not had its version updated
VariantCalling.wdl has not had its version updated
UltimaGenomicsWholeGenomeCramOnly.wdl has not been changed and needs updating
GDCWholeGenomeSomaticSingleSample.wdl has not had its version updated
BroadInternalRNAWithUMIs.wdl has not been changed and needs updating
BroadInternalUltimaGenomics.wdl has not been changed and needs updating
BroadInternalArrays.wdl has not been changed and needs updating
BroadInternalImputation.wdl has not been changed and needs updating
Arrays.wdl has not been changed and needs updating
ValidateChip.wdl has not had its version updated
Imputation.wdl has not been changed and needs updating
IlluminaGenotypingArray.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeReprocessing.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-10-28T19:55:45Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
CheckFingerprint.changelog.md has not been changed and needs to be updated
RNAWithUMIsPipeline.changelog.md has not been changed and needs to be updated
AnnotationFiltration.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeGermline.changelog.md has not been changed and needs to be updated
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartOne.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartTwo.changelog.md has not been changed and needs to be updated
ReblockGVCF.changelog.md has not been changed and needs to be updated
JointGenotyping.changelog.md has not been changed and needs to be updated
UltimaGenomicsJointGenotyping.changelog.md has not been changed and needs to be updated
VariantCalling.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeCramOnly.changelog.md has not been changed and needs to be updated
GDCWholeGenomeSomaticSingleSample.changelog.md has not been changed and needs to be updated
BroadInternalRNAWithUMIs.changelog.md has not been changed and needs to be updated
BroadInternalUltimaGenomics.changelog.md has not been changed and needs to be updated
BroadInternalArrays.changelog.md has not been changed and needs to be updated
BroadInternalImputation.changelog.md has not been changed and needs to be updated
Arrays.changelog.md has not been changed and needs to be updated
ValidateChip.changelog.md has not been changed and needs to be updated
Imputation.changelog.md has not been changed and needs to be updated
IlluminaGenotypingArray.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

nikellepetrillo · 2024-10-30T14:57:49Z

scientific test failures: https://docs.google.com/spreadsheets/d/1J-36kjeRT2N6shkbvwJiFSn_fNJ396J9M6Fd1QqT8Ak/edit?gid=0#gid=0

github-actions · 2024-10-30T16:05:28Z

Remember to squash merge!

github-actions · 2024-10-30T16:05:36Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
RNAWithUMIsPipeline.wdl has not been changed and needs updating
AnnotationFiltration.wdl has not had its version updated
JointGenotypingByChromosomePartOne.wdl has not been changed and needs updating
JointGenotypingByChromosomePartTwo.wdl has not been changed and needs updating
JointGenotyping.wdl has not had its version updated
UltimaGenomicsJointGenotyping.wdl has not had its version updated
GDCWholeGenomeSomaticSingleSample.wdl has not had its version updated
BroadInternalImputation.wdl has not been changed and needs updating
ValidateChip.wdl has not had its version updated
Imputation.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-10-30T16:05:38Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
RNAWithUMIsPipeline.changelog.md has not been changed and needs to be updated
AnnotationFiltration.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeGermline.changelog.md has not been changed and needs to be updated
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartOne.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartTwo.changelog.md has not been changed and needs to be updated
ReblockGVCF.changelog.md has not been changed and needs to be updated
JointGenotyping.changelog.md has not been changed and needs to be updated
UltimaGenomicsJointGenotyping.changelog.md has not been changed and needs to be updated
VariantCalling.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeCramOnly.changelog.md has not been changed and needs to be updated
GDCWholeGenomeSomaticSingleSample.changelog.md has not been changed and needs to be updated
BroadInternalRNAWithUMIs.changelog.md has not been changed and needs to be updated
BroadInternalUltimaGenomics.changelog.md has not been changed and needs to be updated
BroadInternalArrays.changelog.md has not been changed and needs to be updated
BroadInternalImputation.changelog.md has not been changed and needs to be updated
Arrays.changelog.md has not been changed and needs to be updated
ValidateChip.changelog.md has not been changed and needs to be updated
Imputation.changelog.md has not been changed and needs to be updated
IlluminaGenotypingArray.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

nikellepetrillo · 2024-11-01T12:14:22Z

closing as we will use #1405 to update gatk

gatk docker update

b3a4a9a

meganshand reviewed Oct 28, 2024

View reviewed changes

gatk docker update

4de6e1d

adding CompareVcfsVerbosely to Ultima tests

56f8447

nikellepetrillo closed this Nov 1, 2024

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gatk docker update 4.6.1.0 #1403

gatk docker update 4.6.1.0 #1403

nikellepetrillo commented Oct 28, 2024

github-actions bot commented Oct 28, 2024

github-actions bot commented Oct 28, 2024

github-actions bot commented Oct 28, 2024

nikellepetrillo commented Oct 28, 2024 •

edited

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meganshand Oct 28, 2024

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nikellepetrillo commented Oct 30, 2024

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github-actions bot commented Oct 30, 2024

github-actions bot commented Oct 30, 2024

nikellepetrillo commented Nov 1, 2024

gatk docker update 4.6.1.0 #1403

gatk docker update 4.6.1.0 #1403

Conversation

nikellepetrillo commented Oct 28, 2024

Description

Checklist

github-actions bot commented Oct 28, 2024

github-actions bot commented Oct 28, 2024

🔍Version Validation Results:

github-actions bot commented Oct 28, 2024

🔍Changelog Validation Results:

nikellepetrillo commented Oct 28, 2024 • edited Loading

meganshand Oct 28, 2024

Choose a reason for hiding this comment

github-actions bot commented Oct 28, 2024

github-actions bot commented Oct 28, 2024

🔍Version Validation Results:

github-actions bot commented Oct 28, 2024

🔍Changelog Validation Results:

nikellepetrillo commented Oct 30, 2024

github-actions bot commented Oct 30, 2024

github-actions bot commented Oct 30, 2024

🔍Version Validation Results:

github-actions bot commented Oct 30, 2024

🔍Changelog Validation Results:

nikellepetrillo commented Nov 1, 2024

nikellepetrillo commented Oct 28, 2024 •

edited

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