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TSPS-887 make low pass imputation workflow driven by contig input #1803

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Merged
jsotobroad merged 14 commits into from
Apr 1, 2026
+194 −107
Merged

TSPS-887 make low pass imputation workflow driven by contig input #1803

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b6e364e
first pass at making the wdl more contig friendly
Mar 25, 2026
75fe83c
make compute shard and memory task better with this new change
Mar 25, 2026
acc1d35
only need to run split batches once per submission
Mar 25, 2026
28e8813
fix compute memory and shard task
Mar 25, 2026
fd89177
fix sites table suffix and increase memory for bcftools commands
Mar 26, 2026
e0170d8
remove unused optional inputs that are failing and add max retries to…
Mar 27, 2026
96151a6
more memory for bcftools call task and try to fix optional variable p…
Mar 28, 2026
e6b84a3
thihs is dumb
Mar 28, 2026
fe66126
use dumbest fix i can think of
Mar 28, 2026
7fde2e2
figure out mor eoptional inputs
Mar 29, 2026
e63bf8f
Updated pipeline_versions.txt with all pipeline version information
actions-user Mar 30, 2026
ad88646
update changelog
Mar 30, 2026
20151cb
pr feedback1
Apr 1, 2026
bc32bc3
add space aafeter comma
Apr 1, 2026
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2 changes: 1 addition & 1 deletion pipeline_versions.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ BuildIndices 5.1.0 2026-02-13
CramToUnmappedBams 1.1.3 2024-08-02
ExomeGermlineSingleSample 3.2.7 2026-01-21
ExomeReprocessing 3.3.7 2026-01-21
Glimpse2LowPassImputation 0.0.2 2026-03-19
Glimpse2LowPassImputation 0.0.3 2026-03-25
IlluminaGenotypingArray 1.12.27 2026-01-21
Imputation 1.1.23 2025-10-03
ImputationBeagle 3.0.1 2026-02-23
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6 changes: 6 additions & 0 deletions pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.changelog.md
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@@ -1,3 +1,9 @@
# 0.0.3
2026-03-25 (Date of Last Commit)

* Reorganize wdl to be able to run on contigs more easily. Now the workflow is fully driven by the `contigs` input
* The wdl now expects the reference related files to all live under the same cloud base path

# 0.0.2
2026-03-19 (Date of Last Commit)

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