From 9dc718580c4644f2b72d992ba233ebf4336c8509 Mon Sep 17 00:00:00 2001 From: Morgan Taylor Date: Thu, 20 Nov 2025 16:42:04 -0500 Subject: [PATCH 1/3] add glimpse wdl to dockstore --- .dockstore.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.dockstore.yml b/.dockstore.yml index dacc4fc636..468aec27cf 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -50,6 +50,10 @@ workflows: subclass: WDL primaryDescriptorPath: /all_of_us/cmrg/FixItFelixAndVariantCall.wdl + - name: Glimpse2Imputation + subclass: WDL + primaryDescriptorPath: /pipelines/wdl/glimpse/Glimpse2Imputation.wdl + - name: GvsAoUReblockGvcf subclass: WDL primaryDescriptorPath: /all_of_us/cmrg/GvsAoUReblockGvcf.wdl From 9106cbd1066f507db3425a1c246da848753e57fa Mon Sep 17 00:00:00 2001 From: Morgan Taylor Date: Thu, 20 Nov 2025 16:42:42 -0500 Subject: [PATCH 2/3] use mem_gb_phase first --- pipelines/wdl/glimpse/Glimpse2Imputation.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/wdl/glimpse/Glimpse2Imputation.wdl b/pipelines/wdl/glimpse/Glimpse2Imputation.wdl index 92e2d7f268..650170671a 100644 --- a/pipelines/wdl/glimpse/Glimpse2Imputation.wdl +++ b/pipelines/wdl/glimpse/Glimpse2Imputation.wdl @@ -67,7 +67,7 @@ workflow Glimpse2Imputation { preemptible = preemptible, docker = docker, cpu = select_first([cpu_phase, 1]), - mem_gb = select_first([reference_chunk.right, mem_gb_phase]) + mem_gb = select_first([mem_gb_phase, reference_chunk.right]) } } From 69539159e141b83f46082a1be3d5b48b2330c5a6 Mon Sep 17 00:00:00 2001 From: Morgan Taylor Date: Thu, 20 Nov 2025 19:50:56 -0500 Subject: [PATCH 3/3] add changelog --- pipelines/wdl/glimpse/Glimpse2Imputation.changelog.md | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 pipelines/wdl/glimpse/Glimpse2Imputation.changelog.md diff --git a/pipelines/wdl/glimpse/Glimpse2Imputation.changelog.md b/pipelines/wdl/glimpse/Glimpse2Imputation.changelog.md new file mode 100644 index 0000000000..41d04bb996 --- /dev/null +++ b/pipelines/wdl/glimpse/Glimpse2Imputation.changelog.md @@ -0,0 +1,4 @@ +# 0.0.1 +2025-11-20 (Date of Last Commit) + +* Early draft of the pipeline (putting this here to satisfy PR checks for now)