From 09f555e15472b69862ad4093556d9fc3e27a040d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 10 Sep 2026 16:12:24 +0000
Subject: [PATCH 01/11] Bump pip from 23.2.1 to 26.2 in /loading_pipeline

Bumps [pip](https://github.com/pypa/pip) from 23.2.1 to 26.2.
- [Changelog](https://github.com/pypa/pip/blob/main/NEWS.rst)
- [Commits](https://github.com/pypa/pip/compare/23.2.1...26.2)

---
updated-dependencies:
- dependency-name: pip
  dependency-version: '26.2'
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 loading_pipeline/pyproject.toml | 2 +-
 loading_pipeline/uv.lock        | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/loading_pipeline/pyproject.toml b/loading_pipeline/pyproject.toml
index 43c7cbddc6..4cf4c3778a 100644
--- a/loading_pipeline/pyproject.toml
+++ b/loading_pipeline/pyproject.toml
@@ -19,7 +19,7 @@ dependencies = [
     "onnxconverter-common @ git+https://github.com/microsoft/onnxconverter-common.git@f7a8eb699caa6f6a78d3bdfbcaf5dfbd43569ebd",
 
     # Dataproc
-    "pip==23.2.1",
+    "pip==26.2",
     "google-cloud-dataproc==5.16.0",
     "google-cloud-bigquery==3.29.0",
     "google-api-python-client==2.159.0",
diff --git a/loading_pipeline/uv.lock b/loading_pipeline/uv.lock
index d07ecefb95..6fb8b22cc8 100644
--- a/loading_pipeline/uv.lock
+++ b/loading_pipeline/uv.lock
@@ -2843,11 +2843,11 @@ wheels = [
 
 [[package]]
 name = "pip"
-version = "23.2.1"
+version = "26.2"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/ba/19/e63fb4e0d20e48bd2167bb7e857abc0e21679e24805ba921a224df8977c0/pip-23.2.1.tar.gz", hash = "sha256:fb0bd5435b3200c602b5bf61d2d43c2f13c02e29c1707567ae7fbc514eb9faf2", size = 2109449, upload-time = "2023-07-22T09:17:34.056Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/db/96/e6f8e9d9d7b9cc4457092712a7e919c3186aa2c2fa9ffed2c5d29cc947e8/pip-26.2.tar.gz", hash = "sha256:2d8542afcc84cdd8e846c2b36b2861fad1da376dd98f8e7113e9108a3c331690", size = 1848845, upload-time = "2026-07-29T21:57:56.407Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/50/c2/e06851e8cc28dcad7c155f4753da8833ac06a5c704c109313b8d5a62968a/pip-23.2.1-py3-none-any.whl", hash = "sha256:7ccf472345f20d35bdc9d1841ff5f313260c2c33fe417f48c30ac46cccabf5be", size = 2086091, upload-time = "2023-07-22T09:17:31.548Z" },
+    { url = "https://files.pythonhosted.org/packages/62/36/a3aed958d60531cb442b7ab4596cda7b3621cfb916f8ae1d6769795c7dc1/pip-26.2-py3-none-any.whl", hash = "sha256:931c303696af6fa3417112103b1cad26890e5a07eccb5b99783700e33f2b8aad", size = 1816475, upload-time = "2026-07-29T21:57:54.763Z" },
 ]
 
 [[package]]
@@ -4016,7 +4016,7 @@ requires-dist = [
     { name = "jupyter-console", specifier = "==6.6.3" },
     { name = "luigi", specifier = "==3.5.2" },
     { name = "onnxconverter-common", git = "https://github.com/microsoft/onnxconverter-common.git?rev=f7a8eb699caa6f6a78d3bdfbcaf5dfbd43569ebd" },
-    { name = "pip", specifier = "==23.2.1" },
+    { name = "pip", specifier = "==26.2" },
     { name = "pydantic", specifier = "==2.8.2" },
     { name = "qtconsole", specifier = "==5.6.1" },
     { name = "slacker", specifier = "==0.14.0" },

From eae32a9129fc5ed5f70ee90528ccae64f4caf9c6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 10 Sep 2026 16:12:38 +0000
Subject: [PATCH 02/11] Bump cryptography from 46.0.3 to 50.0.0 in
 /loading_pipeline

Bumps [cryptography](https://github.com/pyca/cryptography) from 46.0.3 to 50.0.0.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pyca/cryptography/compare/46.0.3...50.0.0)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-version: 50.0.0
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 loading_pipeline/uv.lock | 108 ++++++++++++++++++---------------------
 1 file changed, 51 insertions(+), 57 deletions(-)

diff --git a/loading_pipeline/uv.lock b/loading_pipeline/uv.lock
index d07ecefb95..2ca8e45a2b 100644
--- a/loading_pipeline/uv.lock
+++ b/loading_pipeline/uv.lock
@@ -883,64 +883,58 @@ toml = [
 
 [[package]]
 name = "cryptography"
-version = "46.0.3"
+version = "50.0.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
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From 04e485ee2b164b1239a360d4dbdc8a6d5b6c669b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 10 Sep 2026 16:13:11 +0000
Subject: [PATCH 03/11] Bump tornado from 6.5.2 to 6.5.8 in /loading_pipeline

Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.5.2 to 6.5.8.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](https://github.com/tornadoweb/tornado/compare/v6.5.2...v6.5.8)

---
updated-dependencies:
- dependency-name: tornado
  dependency-version: 6.5.8
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 loading_pipeline/uv.lock | 28 +++++++++++++---------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/loading_pipeline/uv.lock b/loading_pipeline/uv.lock
index d07ecefb95..93913b5e2e 100644
--- a/loading_pipeline/uv.lock
+++ b/loading_pipeline/uv.lock
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From d0670f6e96d64f9979e0aa8183ec9720fcf32c97 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Fri, 11 Sep 2026 11:54:44 -0400
Subject: [PATCH 04/11] fix package namespacing for build

---
 .github/workflows/pipeline-dev-release.yml  |  2 +-
 .github/workflows/pipeline-prod-release.yml | 13 ++++++++-----
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pipeline-dev-release.yml b/.github/workflows/pipeline-dev-release.yml
index 5c050a9b52..a1c4ec0208 100644
--- a/.github/workflows/pipeline-dev-release.yml
+++ b/.github/workflows/pipeline-dev-release.yml
@@ -1,4 +1,4 @@
-name: dev release
+name: pipeline dev release
 on:
   workflow_run:
     workflows: ["Pipeline Unit Tests"]
diff --git a/.github/workflows/pipeline-prod-release.yml b/.github/workflows/pipeline-prod-release.yml
index 02da04e79e..aec94e31cd 100644
--- a/.github/workflows/pipeline-prod-release.yml
+++ b/.github/workflows/pipeline-prod-release.yml
@@ -1,4 +1,4 @@
-name: prod release
+name: pipeline prod release
 on:
   workflow_run:
     workflows: ["Pipeline Unit Tests"]
@@ -28,8 +28,11 @@ jobs:
 
       - name: build package
         run: |
-          cd loading_pipeline
-          rm -rf dist/
+          rm -rf pipeline_build
+          mkdir pipeline_build
+          cp -r loading_pipeline pipeline_build
+          mv pipeline_build/loading_pipeline/pyproject.toml pipeline_build
+          cd pipeline_build
           python -m pip install build
           python -m build
 
@@ -48,9 +51,9 @@ jobs:
         run: |-
           gcloud storage rm -r gs://seqr-pipeline-runner-builds/prod/latest/ || echo 'No latest release'
           gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/prod/latest/bin/
-          gcloud storage cp loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/prod/latest/pyscripts.zip
+          gcloud storage cp pipeline_build/dist/*.whl gs://seqr-pipeline-runner-builds/prod/latest/pyscripts.zip
           gcloud storage cp loading_pipeline/bin/* gs://seqr-pipeline-runner-builds/prod/${{ github.event.workflow_run.head_sha }}/bin/
-          gcloud storage cp loading_pipeline/dist/*.whl gs://seqr-pipeline-runner-builds/prod/${{ github.event.workflow_run.head_sha }}/pyscripts.zip
+          gcloud storage cp pipeline_build/dist/*.whl gs://seqr-pipeline-runner-builds/prod/${{ github.event.workflow_run.head_sha }}/pyscripts.zip
           gcloud storage cp -r loading_pipeline/var/vep/* gs://seqr-reference-data/vep/
 
   docker:

From 052bf8262e6c859016ec6add80e447b7ca15df1e Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Fri, 11 Sep 2026 13:56:31 -0400
Subject: [PATCH 05/11] execute existing variants export outside dataproc

---
 .../lib/tasks/dataproc/run_pipeline_on_dataproc.py        | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py
index c05730c216..a18247d3a8 100644
--- a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py
+++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc.py
@@ -7,10 +7,18 @@
     BaseRunJobOnDataprocTask,
 )
 from loading_pipeline.lib.tasks.run_pipeline import RunPipelineTask
+from loading_pipeline.lib.tasks.write_existing_variants_parquet import (
+    WriteExistingVariantsParquetTask,
+)
 
 
 @luigi.util.inherits(BaseLoadingRunParams)
 class RunPipelineOnDataprocTask(BaseRunJobOnDataprocTask):
+    attempt_id = luigi.IntParameter()
+
     @property
     def task(self) -> luigi.Task:
         return RunPipelineTask
+
+    def requires(self) -> [luigi.Task]:
+        return [self.clone(WriteExistingVariantsParquetTask), *super().requires()]

From 0b96d92fa679845435fb94063caf44b3a58a2d0e Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Fri, 11 Sep 2026 14:02:29 -0400
Subject: [PATCH 06/11] better naming convention

---
 .../{pipeline-dev-release.yml => dev-pipeline-release.yml}      | 0
 .github/workflows/pipeline-unit-tests.yml                       | 2 +-
 .../{pipeline-prod-release.yml => prod-pipeline-release.yml}    | 0
 3 files changed, 1 insertion(+), 1 deletion(-)
 rename .github/workflows/{pipeline-dev-release.yml => dev-pipeline-release.yml} (100%)
 rename .github/workflows/{pipeline-prod-release.yml => prod-pipeline-release.yml} (100%)

diff --git a/.github/workflows/pipeline-dev-release.yml b/.github/workflows/dev-pipeline-release.yml
similarity index 100%
rename from .github/workflows/pipeline-dev-release.yml
rename to .github/workflows/dev-pipeline-release.yml
diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yml
index 1b989e6335..d26c3f52d1 100644
--- a/.github/workflows/pipeline-unit-tests.yml
+++ b/.github/workflows/pipeline-unit-tests.yml
@@ -9,7 +9,7 @@ on:
       - master
     paths:
       - 'loading_pipeline/**'
-      - '.github/workflows/pipeline-*-release.yaml'
+      - '.github/workflows/*-pipeline-release.yaml'
   pull_request:
     types: [opened, synchronize, reopened]
     paths:
diff --git a/.github/workflows/pipeline-prod-release.yml b/.github/workflows/prod-pipeline-release.yml
similarity index 100%
rename from .github/workflows/pipeline-prod-release.yml
rename to .github/workflows/prod-pipeline-release.yml

From 696ba009df4ab4b2e5f6353917a6a0992503f4ac Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Fri, 11 Sep 2026 14:03:08 -0400
Subject: [PATCH 07/11] update dev release

---
 .github/workflows/dev-pipeline-release.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/dev-pipeline-release.yml b/.github/workflows/dev-pipeline-release.yml
index a1c4ec0208..a884919e38 100644
--- a/.github/workflows/dev-pipeline-release.yml
+++ b/.github/workflows/dev-pipeline-release.yml
@@ -27,8 +27,11 @@ jobs:
 
       - name: Build package
         run: |
-          cd loading_pipeline
-          rm -rf dist/
+          rm -rf pipeline_build
+          mkdir pipeline_build
+          cp -r loading_pipeline pipeline_build
+          mv pipeline_build/loading_pipeline/pyproject.toml pipeline_build
+          cd pipeline_build
           python -m pip install build
           python -m build
 

From ca2421e19f9b0bc690b137832a27c1eb808065d5 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Fri, 11 Sep 2026 14:20:11 -0400
Subject: [PATCH 08/11] fix tests

---
 .../lib/tasks/dataproc/run_pipeline_on_dataproc_test.py  | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py
index a09289a85a..8f6bf6cd02 100644
--- a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py
+++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py
@@ -13,6 +13,9 @@
 from loading_pipeline.lib.test.mock_complete_task import MockCompleteTask
 
 
+@patch(
+    'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.WriteExistingVariantsParquetTask',
+)
 @patch(
     'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask',
 )
@@ -26,6 +29,7 @@ def test_job_already_exists_failed(
         mock_logger: Mock,
         mock_job_controller_client: Mock,
         mock_create_dataproc_cluster: Mock,
+        mock_variants_parquet: Mock,
     ) -> None:
         mock_create_dataproc_cluster.return_value = MockCompleteTask()
         mock_client = mock_job_controller_client.return_value
@@ -63,6 +67,7 @@ def test_job_already_exists_success(
         self,
         mock_job_controller_client: Mock,
         mock_create_dataproc_cluster: Mock,
+        mock_variants_parquet: Mock,
     ) -> None:
         mock_create_dataproc_cluster.return_value = MockCompleteTask()
         mock_client = mock_job_controller_client.return_value
@@ -91,8 +96,10 @@ def test_job_failed(
         mock_logger: Mock,
         mock_job_controller_client: Mock,
         mock_create_dataproc_cluster: Mock,
+        mock_variants_parquet: Mock,
     ) -> None:
         mock_create_dataproc_cluster.return_value = MockCompleteTask()
+        mock_variants_parquet.return_value = MockCompleteTask()
         mock_client = mock_job_controller_client.return_value
         mock_client.get_job.side_effect = [
             google.api_core.exceptions.NotFound(
@@ -139,8 +146,10 @@ def test_job_success(
         mock_logger: Mock,
         mock_job_controller_client: Mock,
         mock_create_dataproc_cluster: Mock,
+        mock_variants_parquet: Mock,
     ) -> None:
         mock_create_dataproc_cluster.return_value = MockCompleteTask()
+        mock_variants_parquet.return_value = MockCompleteTask()
         mock_client = mock_job_controller_client.return_value
         mock_client.get_job.side_effect = [
             google.api_core.exceptions.NotFound(

From 2786c23e2641d53c6a6782b523a567d5211f6701 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Fri, 11 Sep 2026 14:36:10 -0400
Subject: [PATCH 09/11] fix mock path

---
 .../lib/tasks/dataproc/run_pipeline_on_dataproc_test.py         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py
index 8f6bf6cd02..f10ce92942 100644
--- a/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py
+++ b/loading_pipeline/lib/tasks/dataproc/run_pipeline_on_dataproc_test.py
@@ -14,7 +14,7 @@
 
 
 @patch(
-    'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.WriteExistingVariantsParquetTask',
+    'loading_pipeline.lib.tasks.dataproc.run_pipeline_on_dataproc.WriteExistingVariantsParquetTask',
 )
 @patch(
     'loading_pipeline.lib.tasks.dataproc.base_run_job_on_dataproc.CreateDataprocClusterTask',

From 95e8cce651c8e07845222a0264a075406fcc67b1 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Fri, 11 Sep 2026 14:53:08 -0400
Subject: [PATCH 10/11] test fix

---
 loading_pipeline/lib/tasks/dataproc/misc_test.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/loading_pipeline/lib/tasks/dataproc/misc_test.py b/loading_pipeline/lib/tasks/dataproc/misc_test.py
index b9c049005a..1c29daa4d6 100644
--- a/loading_pipeline/lib/tasks/dataproc/misc_test.py
+++ b/loading_pipeline/lib/tasks/dataproc/misc_test.py
@@ -31,8 +31,6 @@ def test_to_kebab_str_args(self, _: Mock):
                 'SNV_INDEL',
                 '--run-id',
                 'a_misc_run',
-                '--attempt-id',
-                '0',
                 '--sample-type',
                 'WGS',
                 '--callset-path',
@@ -47,5 +45,7 @@ def test_to_kebab_str_args(self, _: Mock):
                 '[]',
                 '--is-new-gcnv-joint-call',
                 'False',
+                '--attempt-id',
+                '0',
             ],
         )

From bac5630330fb96333a04135e2561dc3a59920d93 Mon Sep 17 00:00:00 2001
From: Hana Snow <hsnow@broadinstitute.org>
Date: Mon, 14 Sep 2026 15:15:28 -0400
Subject: [PATCH 11/11] fix .yaml extension

---
 .../{dev-pipeline-release.yml => dev-pipeline-release.yaml}       | 0
 .../{pipeline-unit-tests.yml => pipeline-unit-tests.yaml}         | 0
 .../{prod-pipeline-release.yml => prod-pipeline-release.yaml}     | 0
 3 files changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{dev-pipeline-release.yml => dev-pipeline-release.yaml} (100%)
 rename .github/workflows/{pipeline-unit-tests.yml => pipeline-unit-tests.yaml} (100%)
 rename .github/workflows/{prod-pipeline-release.yml => prod-pipeline-release.yaml} (100%)

diff --git a/.github/workflows/dev-pipeline-release.yml b/.github/workflows/dev-pipeline-release.yaml
similarity index 100%
rename from .github/workflows/dev-pipeline-release.yml
rename to .github/workflows/dev-pipeline-release.yaml
diff --git a/.github/workflows/pipeline-unit-tests.yml b/.github/workflows/pipeline-unit-tests.yaml
similarity index 100%
rename from .github/workflows/pipeline-unit-tests.yml
rename to .github/workflows/pipeline-unit-tests.yaml
diff --git a/.github/workflows/prod-pipeline-release.yml b/.github/workflows/prod-pipeline-release.yaml
similarity index 100%
rename from .github/workflows/prod-pipeline-release.yml
rename to .github/workflows/prod-pipeline-release.yaml