[DRAFT] TSPS-183 Beagle imputation hg38 wdl and associated support wdls #1333

mmorgantaylor · 2024-07-15T19:26:48Z

Description

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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 documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.

Did you add inputs, outputs, or tasks to a workflow?
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If you made a changelog update, did you update the pipeline version number?

dsde-jenkins · 2024-07-15T19:26:51Z

Can one of the admins verify this patch?

github-actions · 2024-07-15T19:27:01Z

Remember to squash merge!

github-actions · 2024-07-15T19:27:13Z

🔍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
UltimaGenomicsWholeGenomeCramOnly.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
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
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
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 · 2024-07-15T19:27:14Z

🔍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 been changed and needs updating
UltimaGenomicsWholeGenomeCramOnly.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
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
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.changelog.md: No such file or directory
ImputationBeagle.wdl and ImputationBeagle.changelog.md do not have matching versions
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.changelog.md: No such file or directory
ImputationBeaglePreChunk.wdl and ImputationBeaglePreChunk.changelog.md do not have matching versions
CreateImputationRefPanelBeagle.wdl has not had its version updated
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.changelog.md: No such file or directory
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.changelog.md: No such file or directory
LiftoverVcfs.wdl and LiftoverVcfs.changelog.md do not have matching versions
Imputation.wdl has not had its version updated
Arrays.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-07-19T16:51:20Z

Remember to squash merge!

github-actions · 2024-07-19T16:51:31Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
snm3C.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
Multiome.changelog.md has not been changed and needs to be updated
atac.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
VariantCalling.changelog.md has not been changed and needs to be updated
ReblockGVCF.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeCramOnly.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
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
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
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 · 2024-07-19T16:51:31Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
snm3C.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
Multiome.wdl has not been changed and needs updating
atac.wdl has not been changed and needs updating
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 been changed and needs updating
ReblockGVCF.wdl has not been changed and needs updating
UltimaGenomicsWholeGenomeCramOnly.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
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
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.changelog.md: No such file or directory
ImputationBeagle.wdl and ImputationBeagle.changelog.md do not have matching versions
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.changelog.md: No such file or directory
ImputationBeaglePreChunk.wdl and ImputationBeaglePreChunk.changelog.md do not have matching versions
CreateImputationRefPanelBeagle.wdl has not had its version updated
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.changelog.md: No such file or directory
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.changelog.md: No such file or directory
LiftoverVcfs.wdl and LiftoverVcfs.changelog.md do not have matching versions
Imputation.wdl has not had its version updated
Arrays.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-07-26T15:14:55Z

Remember to squash merge!

github-actions · 2024-07-26T15:15:05Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
snm3C.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeCramOnly.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
WholeGenomeGermlineSingleSample.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
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
BroadInternalRNAWithUMIs.changelog.md has not been changed and needs to be updated
BroadInternalUltimaGenomics.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
CheckFingerprint.changelog.md has not been changed and needs to be updated
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
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 · 2024-07-26T15:15:06Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
Multiome.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
snm3C.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
atac.wdl has not been changed and needs updating
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
UltimaGenomicsWholeGenomeCramOnly.wdl has not been changed and needs updating
VariantCalling.wdl has not been changed and needs updating
ReblockGVCF.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
UltimaGenomicsWholeGenomeGermline.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
BroadInternalRNAWithUMIs.wdl has not been changed and needs updating
BroadInternalUltimaGenomics.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
CheckFingerprint.wdl has not been changed and needs updating
CreateImputationRefPanelBeagle.wdl has not had its version updated
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/CreateImputationRefPanelBeagle.changelog.md: No such file or directory
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.changelog.md: No such file or directory
LiftoverVcfs.wdl and LiftoverVcfs.changelog.md do not have matching versions
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.changelog.md: No such file or directory
ImputationBeagle.wdl and ImputationBeagle.changelog.md do not have matching versions
grep: /home/runner/work/warp/warp/pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.changelog.md: No such file or directory
ImputationBeaglePreChunk.wdl and ImputationBeaglePreChunk.changelog.md do not have matching versions
Imputation.wdl has not had its version updated
Arrays.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

jessicaway · 2024-11-13T16:18:29Z

@mmorgantaylor is this still relevant?

mmorgantaylor · 2024-11-13T17:10:53Z

@jessicaway yes this is our working branch for beagle imputation for the imputation service. cc @jsotobroad. Jess, would it be helpful for us to squash and rebase off of develop?

jessicaway · 2024-11-13T21:20:41Z

OK, no problem! Whatever works best is fine. We were just cleaning up PRs and thought we would check in. I don't think we have touched imputation much recently, so I don't anticipate any conflicts

*pre splitting and prechunking beagle imputation inputs to lower log numbers and storage account egress --------- Co-authored-by: Jose Soto <[email protected]>

…istic (#1285) * remove multi sample vcf index workflow input and add it to the PreSplitVcf task. add seed number so that beagle is always deterministic. add comment to cpu input for PhaseAndImputeBeagle task * change output_callset_name to output_base_name and remove optional outputs * change n_failed_chunks ticket to an int --------- Co-authored-by: Jose Soto <[email protected]>

* clean up wdl with stuff from TSPS-241 * try to make fail fast work with double nested scatters --------- Co-authored-by: Jose Soto <[email protected]>

…ng imputation against it (#1296) * add optional error count override for testing * rename reference base prefix variable and make it more user friendly --------- Co-authored-by: Jose Soto <[email protected]>

* try auto specifying chr at end of basename * both tasks * add liftovervcfs to dockstore * allow specifying max mem

* try creating bed files * try again * try again again * a different thing * use bedtools and bed ref panel files * oops update the correct task * fix * use the right freaking file name * remove comment

update ImputationBeagle

* add array imputation quota consumed wdl * add changelogs for imputation array related workflows --------- Co-authored-by: Jose Soto <[email protected]>

* changes to help beagle imputation wdl run on a 400k sample reference panel --------- Co-authored-by: Jose Soto <[email protected]> * remove create imputation ref panel beagle wdl and changelog * PR feedback --------- Co-authored-by: Jose Soto <[email protected]> Co-authored-by: M. Morgan Aster <[email protected]>

Co-authored-by: Jose Soto <[email protected]>

…nel (#1468) * remove tasks for recovering variants not in the reference panel and separate out beagle tasks from imputation tasks * remove prechunk wdl and references to it remove "Beagle" from task names in BeagleTasks.wdl --------- Co-authored-by: Jose Soto <[email protected]>

github-actions · 2025-02-13T21:45:00Z

Remember to squash merge!

github-actions · 2025-02-13T21:45:10Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
SlideSeq.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
ReblockGVCF.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.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
VariantCalling.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeCramOnly.changelog.md has not been changed and needs to be updated
CheckFingerprint.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
BroadInternalUltimaGenomics.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
ExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-02-13T21:45:12Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not been changed and needs updating
Imputation.wdl has not had its version updated
Arrays.wdl has not been changed and needs updating
ReblockGVCF.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
UltimaGenomicsWholeGenomeGermline.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
CheckFingerprint.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
BroadInternalUltimaGenomics.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
ExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

pullapprove bot requested review from fleharty, gbggrant, kachulis and samuelklee July 15, 2024 19:26

mmorgantaylor added 13 commits February 13, 2025 16:40

wip add beagle imputation stuff

271ee3a

add 2 wdls to dockstore.yml

1dd65d5

fix docker gar url

13c6d96

use the right path for jars

5d7ce46

wip on imputation wdl

bf1d66c

oops use correct jar

93af115

missing equals

318740c

fix java call again

63f50a1

fix java call

85981d6

oops match file names

2d90979

update beagle jar to 01Mar24.d36

47e36a5

debug GatherVcfs

2c198ae

debug GatherVcfs 2

3ce80bb

mmorgantaylor and others added 25 commits February 13, 2025 16:40

add output to test

2097144

next test

dadf37a

more test

1a3c7da

another test

b679d0e

update real task

4b1f8de

TSPS-226 presplit and prechunk beagle inputs (#1272)

fa2846e

*pre splitting and prechunking beagle imputation inputs to lower log numbers and storage account egress --------- Co-authored-by: Jose Soto <[email protected]>

rename workflow

4ba418f

TSPS-241 Clean up beagle wdl (#1288)

51093ba

* clean up wdl with stuff from TSPS-241 * try to make fail fast work with double nested scatters --------- Co-authored-by: Jose Soto <[email protected]>

add specific gatk_docker

2944cb9

TSPS-142 updates to help creating simulated reference panel and runni…

43e98ac

…ng imputation against it (#1296) * add optional error count override for testing * rename reference base prefix variable and make it more user friendly --------- Co-authored-by: Jose Soto <[email protected]>

add maxRetries 2 to all imputation beagle tasks

e7faec2

add prechunk wdl to dockstore

79cdeab

use acr for default ubuntu image

8da5c2f

add preemptible 3

ace2278

use acr gatk docker as default

6f86d5d

don't use preemptibles on GatherVcfs

c9210ec

basename fix for imputation beagle ref panel generation (#1332)

279dcca

* try auto specifying chr at end of basename * both tasks * add liftovervcfs to dockstore * allow specifying max mem

TSPS-269 Speed up CountVariantsInChunksBeagle by using bedtools (#1335)

d7a0829

* try creating bed files * try again * try again again * a different thing * use bedtools and bed ref panel files * oops update the correct task * fix * use the right freaking file name * remove comment

update pipeline version to 0.0.2

444b60d

TSPS-293: Fix up streaming imputation beagle (#1347)

4e6593e

update ImputationBeagle

add array imputation quota consumed wdl (#1425)

9cadb1b

* add array imputation quota consumed wdl * add changelogs for imputation array related workflows --------- Co-authored-by: Jose Soto <[email protected]>

add set -e -o pipefail to all relevant imputation tasks (#1434)

4a345be

Co-authored-by: Jose Soto <[email protected]>

mmorgantaylor force-pushed the TSPS-183_mma_beagle_imputation_hg38 branch from 79d3510 to eaeabdc Compare February 13, 2025 21:44

Updated pipeline_versions.txt with all pipeline version information

4f107d0

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[DRAFT] TSPS-183 Beagle imputation hg38 wdl and associated support wdls #1333

[DRAFT] TSPS-183 Beagle imputation hg38 wdl and associated support wdls #1333

mmorgantaylor commented Jul 15, 2024

dsde-jenkins commented Jul 15, 2024

github-actions bot commented Jul 15, 2024

github-actions bot commented Jul 15, 2024

github-actions bot commented Jul 15, 2024

github-actions bot commented Jul 19, 2024

github-actions bot commented Jul 19, 2024

github-actions bot commented Jul 19, 2024

github-actions bot commented Jul 26, 2024

github-actions bot commented Jul 26, 2024

github-actions bot commented Jul 26, 2024

jessicaway commented Nov 13, 2024

mmorgantaylor commented Nov 13, 2024

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[DRAFT] TSPS-183 Beagle imputation hg38 wdl and associated support wdls #1333

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[DRAFT] TSPS-183 Beagle imputation hg38 wdl and associated support wdls #1333

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mmorgantaylor commented Jul 15, 2024

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