updating gatk to version 4.6.0.0 #1313

meganshand · 2024-07-01T16:13:21Z

There are changes in the most recent GATK release that I'd like for the BGE pipeline, so this is a draft PR that changes it everywhere from 4.5.0.0 -> 4.6.0.0 so that I can track broken tests in a centralized place (which we expect for at least the JointGenotyping pipelines).

github-actions · 2024-07-01T16:13:32Z

Remember to squash merge!

github-actions · 2024-07-01T16:13:42Z

🔍Version Validation Results:

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

github-actions · 2024-07-01T16:13:42Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-02T14:44:01Z

Remember to squash merge!

github-actions · 2024-07-02T14:44:12Z

🔍Version Validation Results:

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

github-actions · 2024-07-02T14:44:12Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-03T14:06:51Z

Remember to squash merge!

github-actions · 2024-07-03T14:07:01Z

🔍Version Validation Results:

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

github-actions · 2024-07-03T14:07:04Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-08T20:04:49Z

Remember to squash merge!

github-actions · 2024-07-08T20:05:01Z

🔍Version Validation Results:

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

github-actions · 2024-07-08T20:05:01Z

🔍Changelog Validation Results:

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

meganshand · 2024-07-11T12:49:39Z

retest this please

github-actions · 2024-07-12T12:26:47Z

Remember to squash merge!

github-actions · 2024-07-12T12:26:59Z

🔍Version Validation Results:

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

github-actions · 2024-07-12T12:27:00Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-18T15:15:18Z

Remember to squash merge!

github-actions · 2024-07-18T15:15:31Z

🔍Version Validation Results:

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

github-actions · 2024-07-18T15:15:33Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-18T15:28:52Z

Remember to squash merge!

github-actions · 2024-07-18T15:29:03Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-18T15:29:05Z

🔍Version Validation Results:

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

github-actions · 2024-07-19T14:26:16Z

Remember to squash merge!

github-actions · 2024-09-04T18:05:42Z

🔍Changelog Validation Results:

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

github-actions · 2024-09-04T18:05:44Z

🔍Version Validation Results:

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

meganshand · 2024-09-05T20:04:26Z

All Scientific test differences are now accounted for! The changes are addressed here: broadinstitute/gatk#8973

The major differences are:

In the ExomeGermlineSingleSample, ExomeReprocessing, JointGenotyping, ReblockGvcf, WholeGenomeGermlineSingleSample, and WholeGenomeRepprocessing pipelines we see the following expected differences:

Expected 0/0 -> ./. (no call genotype) changes in ReblockGVCFs and JointCalling. This also changes the AN annotation.
HaplotypeCaller drops some low quality variant calls. This occurs before Reblocking, so the only difference we see in the ReblockedGVCF (that already dropped this site) is a change in DP for the genotype.
If AD is 0 for non-ref reads (which happens with DRAGEN inputs) then AS_QD will have jitter because the AS_QD is calculated to be infinity. These sites have expected AS_QD differences (that are frequently quite different from QD since that doesn’t use AD for the depth calculation)
Dragen mode pipelines have small differences from both dragmap non-determinism and small changes to HaplotypeCaller at low quality sites.

In the UltimaGenomicsJointGenotyping and UltimaGenomicsWholeGenomeGermline pipelines we see the following expected differences:

Bug fix to UltimaJointGenotyping pipeline. Some sites had the wrong number of values in the allele specific annotations, but this is now fixed.
Ultima single sample pipeline has some expected differences in the single sample calls from a HaplotypeCaller change.

Therefore the Scientific tests that will need to be updated are the following:

BroadInternalUltimaGenomics
ExomeGermlineSingleSample
ExomeReprocessing
JointGenotyping
ReblockGvcf
UltimaGenomicsJointGenotyping
UltimaGenomicsWholeGenomeGermline
WholeGenomeGermlineSingleSample
WholeGenomeRepprocessing

I will take a stab at updating the change logs to reflect at least the pipelines with significant changes and clean up a few things and then this will be ready for review.

github-actions · 2024-09-06T12:10:42Z

Remember to squash merge!

github-actions · 2024-09-06T12:10:52Z

🔍Version Validation Results:

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

github-actions · 2024-09-06T12:10:55Z

🔍Changelog Validation Results:

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

github-actions · 2024-09-06T12:19:10Z

Remember to squash merge!

github-actions · 2024-09-06T12:19:20Z

🔍Version Validation Results:

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

github-actions · 2024-09-06T12:19:21Z

🔍Changelog Validation Results:

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

github-actions · 2024-09-06T13:04:40Z

Remember to squash merge!

github-actions · 2024-09-06T13:04:48Z

🔍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 · 2024-09-06T13:04:55Z

🔍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 · 2024-09-06T15:45:41Z

Remember to squash merge!

github-actions · 2024-09-06T15:45:51Z

🔍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 · 2024-09-06T15:45:53Z

🔍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 · 2024-09-08T11:49:33Z

Remember to squash merge!

github-actions · 2024-09-08T11:49:41Z

🔍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.

github-actions · 2024-09-08T11:49:43Z

🔍Changelog Validation Results:

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

pullapprove bot requested review from chipstewart, fleharty, gbggrant, kachulis and samuelklee July 1, 2024 16:13

meganshand force-pushed the ms_gatk_4600 branch from b58e15d to 1f38183 Compare July 18, 2024 15:15

meganshand force-pushed the ms_gatk_4600 branch from 8daa95c to 879f699 Compare July 19, 2024 14:26

Merge branch 'develop' into ms_gatk_4600

927a354

Updated pipeline_versions.txt with all pipeline version information

f1802da

cleaning up verboseVCF checks

abce09f

changelogs

c23d880

Updated pipeline_versions.txt with all pipeline version information

d05057e

meganshand marked this pull request as ready for review September 6, 2024 13:14

updated changlogs and wdl versions

77a645c

Updated pipeline_versions.txt with all pipeline version information

2667c11

Merge branch 'develop' into ms_gatk_4600

7cf95e7

Updated pipeline_versions.txt with all pipeline version information

a731569

nikellepetrillo merged commit bc8c97d into develop Sep 10, 2024
5 of 6 checks passed

meganshand deleted the ms_gatk_4600 branch September 10, 2024 14:25

updating gatk to version 4.6.0.0 #1313

updating gatk to version 4.6.0.0 #1313

Conversation

meganshand commented Jul 1, 2024

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🔍Version Validation Results:

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🔍Changelog Validation Results:

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🔍Changelog Validation Results:

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🔍Changelog Validation Results:

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🔍Changelog Validation Results:

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🔍Version Validation Results:

github-actions bot commented Sep 8, 2024

🔍Changelog Validation Results: