TSPS-797 check in glimpse pipeline (#1788)

* add first pass of glimpse low pass imputation wdl.

---------

Co-authored-by: Morgan Taylor <marymorg@broadinstitute.org>
Co-authored-by: Jose Soto <jsoto@broadinstitute.org>
Co-authored-by: GitHub Action <action@github.com>

Author: 4 people

.dockstore.yml

@@ -4,11 +4,11 @@ workflows:
   - name: aggregate_rsem_results
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/aggregate_rsem_results.wdl
- 
+
   - name: AggregateSusieWorkflow
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/AggregateSusieWorkflow.wdl
- 
+
   - name: ArrayImputationQuotaConsumed
     subclass: WDL
     primaryDescriptorPath: /pipelines/wdl/arrays/imputation_beagle/ArrayImputationQuotaConsumed.wdl
@@ -25,19 +25,19 @@ workflows:
   - name: Beagle5Phasing
     subclass: WDL
     primaryDescriptorPath: /all_of_us/phasing/Beagle5Phasing.wdl
-  
+
   - name: BuildIndices
     subclass: WDL
     primaryDescriptorPath: /pipelines/wdl/build_indices/BuildIndices.wdl
 
   - name: CalculatePhenotypeGroups
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/CalculatePhenotypeGroups.wdl
-  
+
   - name: convert_vcf_to_plink_bed
     subclass: WDL
     primaryDescriptorPath: /all_of_us/admixture/convert_vcf_to_plink_bed.wdl
-  
+
   - name: CramToUnmappedBams
     subclass: WDL
     primaryDescriptorPath: /pipelines/wdl/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl
@@ -66,6 +66,10 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /all_of_us/cmrg/FixItFelixAndVariantCall.wdl
 
+  - name: Glimpse2LowPassImputation
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.wdl
+
   - name: get_wgs_median_coverage
     subclass: WDL
     primaryDescriptorPath: /all_of_us/mitochondria/get_wgs_median_coverage.wdl
@@ -216,7 +220,7 @@ workflows:
   - name: SusieR_Workflow
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/susieR_workflow.wdl
-  
+
   - name: TestArrayImputationQC
     subclass: WDL
     primaryDescriptorPath: /verification/test-wdls/TestArrayImputationQC.wdl

pipeline_versions.txt

@@ -4,6 +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	 0.0.1	2026-02-26 
 IlluminaGenotypingArray	 1.12.27	2026-01-21 
 Imputation	 1.1.23	2025-10-03 
 ImputationBeagle	 3.0.1	2026-02-23 

pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.changelog.md

@@ -0,0 +1,4 @@
+# 0.0.1
+2026-02-26 (Date of Last Commit)
+
+* Early draft of the glimpse lowpass imputation pipeline (putting this here to satisfy PR checks for now)