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Reducing memory required for ValidateVCF in Reblock pipeline #1400

Merged
merged 5 commits into from
Oct 30, 2024
Merged

Reducing memory required for ValidateVCF in Reblock pipeline #1400

merged 5 commits into from
Oct 30, 2024

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meganshand
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In the ReblockGVCFs pipeline, there is a step to validate the reblocked GVCF. If the user does not provide an interval list to validate over, then the pipeline uses the input GVCF itself as the interval list to validate over. This frequently occurs with DRAGEN whole genome GVCFs since there isn't an associated interval list, and DRAGEN drops some regions so a generic WGS interval list cannot be used.

By adding the argument --VARIANT_ID_METHOD USE_FIRST to the command, the method in htsjdk that combines adjacent intervals requires much less memory.

@github-actions GitHub Actions
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Remember to squash merge!

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🔍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
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
ReblockGVCF.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
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
Arrays.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

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🔍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
UltimaGenomicsWholeGenomeGermline.wdl has not been changed and needs updating
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
ReblockGVCF.wdl has not been changed and needs updating
VariantCalling.wdl has not been changed and needs updating
UltimaGenomicsWholeGenomeCramOnly.wdl has not been changed and needs updating
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
Arrays.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 GitHub Actions
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Remember to squash merge!

@github-actions GitHub Actions
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🔍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
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
ReblockGVCF.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
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
Arrays.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

@github-actions GitHub Actions
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🔍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
UltimaGenomicsWholeGenomeGermline.wdl has not been changed and needs updating
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
ReblockGVCF.wdl has not been changed and needs updating
VariantCalling.wdl has not been changed and needs updating
UltimaGenomicsWholeGenomeCramOnly.wdl has not been changed and needs updating
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
Arrays.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 GitHub Actions
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Remember to squash merge!

@github-actions GitHub Actions
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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 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.

@nikellepetrillo
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retest this please

@github-actions GitHub Actions
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Remember to squash merge!

@github-actions 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.

@github-actions GitHub Actions
Copy link

🔍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.

@nikellepetrillo nikellepetrillo merged commit 672993e into develop Oct 30, 2024
12 checks passed
@meganshand meganshand deleted the ms_reblock branch October 30, 2024 14:20
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@nikellepetrillo nikellepetrillo nikellepetrillo approved these changes

@jessicaway jessicaway jessicaway approved these changes

@aawdeh aawdeh aawdeh approved these changes

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@meganshand @nikellepetrillo @aawdeh @jessicaway @actions-user