diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index f4b3e60..b4e8756 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -14,7 +14,7 @@ jobs:
         runtime: [docker, conda]
     permissions:
       id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@trs/pathogen-repo-build/wait-for-aws-batch-job
     secrets: inherit
     with:
       runtime: ${{ matrix.runtime }}
diff --git a/.github/workflows/fetch-and-ingest-branch.yaml b/.github/workflows/fetch-and-ingest-branch.yaml
index fe00531..4488bdb 100644
--- a/.github/workflows/fetch-and-ingest-branch.yaml
+++ b/.github/workflows/fetch-and-ingest-branch.yaml
@@ -28,7 +28,7 @@ jobs:
     needs: [set_config_overrides]
     permissions:
       id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@trs/pathogen-repo-build/wait-for-aws-batch-job
     secrets: inherit
     with:
       runtime: aws-batch
diff --git a/.github/workflows/fetch-and-ingest.yaml b/.github/workflows/fetch-and-ingest.yaml
index d7b4d27..cd86e79 100644
--- a/.github/workflows/fetch-and-ingest.yaml
+++ b/.github/workflows/fetch-and-ingest.yaml
@@ -35,7 +35,7 @@ jobs:
   fetch-and-ingest:
     permissions:
       id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@trs/pathogen-repo-build/wait-for-aws-batch-job
     secrets: inherit
     with:
       runtime: aws-batch
diff --git a/.github/workflows/rebuild-hmpxv1-big.yaml b/.github/workflows/rebuild-hmpxv1-big.yaml
index e8f3f23..872d42a 100644
--- a/.github/workflows/rebuild-hmpxv1-big.yaml
+++ b/.github/workflows/rebuild-hmpxv1-big.yaml
@@ -23,7 +23,7 @@ jobs:
   rebuild_hmpxv1_big:
     permissions:
       id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@trs/pathogen-repo-build/wait-for-aws-batch-job
     secrets: inherit
     with:
       runtime: aws-batch
diff --git a/.github/workflows/rebuild-hmpxv1.yaml b/.github/workflows/rebuild-hmpxv1.yaml
index 75c931e..1698793 100644
--- a/.github/workflows/rebuild-hmpxv1.yaml
+++ b/.github/workflows/rebuild-hmpxv1.yaml
@@ -23,7 +23,7 @@ jobs:
   rebuild_hmpxv1:
     permissions:
       id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@trs/pathogen-repo-build/wait-for-aws-batch-job
     secrets: inherit
     with:
       runtime: aws-batch
diff --git a/.github/workflows/rebuild-mpxv.yaml b/.github/workflows/rebuild-mpxv.yaml
index 4650af3..03ed061 100644
--- a/.github/workflows/rebuild-mpxv.yaml
+++ b/.github/workflows/rebuild-mpxv.yaml
@@ -23,7 +23,7 @@ jobs:
   rebuild_mpxv:
     permissions:
       id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@trs/pathogen-repo-build/wait-for-aws-batch-job
     secrets: inherit
     with:
       runtime: aws-batch