diff --git a/.github/workflows/1-Build-Dependencies-Image.yaml b/.github/workflows/1-Build-Dependencies-Image.yaml
new file mode 100644
index 0000000..4052605
--- /dev/null
+++ b/.github/workflows/1-Build-Dependencies-Image.yaml
@@ -0,0 +1,74 @@
+name: Build Dependencies Container Image
+run-name: (1) Dependencies Image Build - ${{ github.event.head_commit.message }} - ${{ github.ref_name }}
+
+# This GitHub Actions workflow builds a Dependencies Docker image for the
+# cfa-epinow2-pipeline-docker project.
+#
+# - The `build_image_dependencies` job carries out the first part of a
+#   multi-stage build. It downloads and installs all the dependencies
+#   listed in the `DESCRIPTION` file. It uses the `Dockerfile-dependencies`
+#   file to build the image.
+#
+#   The built image is then pushed to the corresponding registry.
+#
+#   The process is cached to avoid rebuilding the image if the dependencies
+#   have not changed. This is by hashing the `DESCRIPTION` file and the
+#   `Dockerfile-dependencies` file.
+
+# - This built docker image is then referenced by the simply named 'Dockerfile', built in:
+#     - "2_pre-Test-Model-Image-Build" and
+#     - "2-Run-Epinow2-Pipeline.yaml"
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "./Dockerfile-dependencies" # the dockerfile this workflow builds from
+      - "./.github/workflows/build-dependency-image.yaml" # this workflow
+
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "./Dockerfile-dependencies" # the dockerfile this workflow builds from
+      - "./.github/workflows/build-dependency-image.yaml" # this workflow
+
+  workflow_dispatch:
+
+env:
+  # Together, these form: cfaprdbatchcr.azurecr.io/cfa-epinow2-pipeline
+  REGISTRY: cfaprdbatchcr.azurecr.io
+  IMAGE_NAME: cfa-epinow2-pipeline
+
+jobs:
+  Job01-build_image_dependencies:
+    runs-on: cfa-cdcgov # VM based runner serving CFA's cdcgov repos (as opposed to cdcent)
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Check cache
+        uses: actions/cache@v3
+        id: cache
+        with:
+          key: docker-dependencies-${{ runner.os }}-${{ hashFiles('./DESCRIPTION', './Dockerfile-dependencies') }}
+          path:
+            ./DESCRIPTION
+
+      - name: Login to the Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: "cfaprdbatchcr.azurecr.io"
+          username: "cfaprdbatchcr"
+          password: ${{ secrets.CFAPRDBATCHCR_REGISTRY_PASSWORD }}
+
+      - name: Build and push
+        if: steps.cache.outputs.cache-hit != 'true'
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          tags: |
+            ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}-dependencies:latest
+            ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}-dependencies:${{ github.sha }}
+          file: ./Dockerfile-dependencies
diff --git a/.github/workflows/2-Run-Epinow2-Pipeline.yaml b/.github/workflows/2-Run-Epinow2-Pipeline.yaml
new file mode 100644
index 0000000..d580194
--- /dev/null
+++ b/.github/workflows/2-Run-Epinow2-Pipeline.yaml
@@ -0,0 +1,116 @@
+name: Run Epinow2 Pipeline
+run-name: (2) Pipeline - "${{ github.event.head_commit.message }}"
+
+# This GitHub Actions workflow builds a Docker image for the
+# cfa-epinow2-pipeline-docker project.
+#
+# - The build_image job builds the final image using the `Dockerfile` file.
+#   It uses the image built in "1-Build-Dependencies-Image.yaml" as a base image.
+#
+#   During the build process, the package is installed and built. Furthermore
+#   the package is checked using `R CMD check` to ensure that it is working
+#   correctly.
+#
+#   Once the image is built, it is pushed to the corresponding registry.
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+  schedule:
+    - cron: "0 12 * * 3"
+
+env:
+  # Together, these form: cfaprdbatchcr.azurecr.io/cfa-epinow2-pipeline
+  REGISTRY: cfaprdbatchcr.azurecr.io
+  IMAGE_NAME: cfa-epinow2-pipeline
+
+jobs:
+
+  _01_build-model-image:
+    runs-on: cfa-cdcgov #
+    steps:
+
+      - name: Login to the Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: "cfaprdbatchcr.azurecr.io"
+          username: "cfaprdbatchcr"
+          password: ${{ secrets.CFAPRDBATCHCR_REGISTRY_PASSWORD }}
+
+      # Comment out if you want to just test the pool creation without waiting for build and push
+      - name: Build and push model pipeline image for Azure batch # second stage, the actual payload
+        id: build_and_push_model_image
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          tags: |
+            ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}:latest
+            ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}:${{ github.sha }}
+          file: ./Dockerfile # second stage Dockerfile
+
+  _02_create-batch-pool-and-submit-jobs:
+    runs-on: cfa-cdcgov
+    needs:
+      - _01_build-model-image
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout Repo
+        id: checkout_repo
+        uses: actions/checkout@v4
+
+      - name: Login to Azure with NNH Service Principal
+        id: azure_login_2
+        uses: azure/login@v2
+        with:
+        # managed by EDAV. Contact Amit Mantri or Jon Kislin if you have issues.
+          creds: ${{ secrets.EDAV_CFA_PREDICT_NNHT_SP }}
+
+
+      - name: Get Github Short sha
+        run: |
+          shortSHA=$(git rev-parse --short ${{ github.sha }})
+          echo "SHORT_SHA=$shortSHA" >> $GITHUB_ENV
+
+      - name: Create cfa-epinow2-pipeline Pool
+        id: create_batch_pool
+
+        # Every Azure Batch Pool parameter can simply go here,
+        # no python module or config toml necessary
+        env:
+          POOL_ID:           "cfa-epinow2-${{ env.SHORT_SHA }}" # version the pools with the github sha
+          BATCH_ACCOUNT:     "cfaprdba"
+          BATCH_ENDPOINT:    "https://cfaprdba.eastus.batch.azure.com/"
+          VM_IMAGE_TAG:      "canonical:0001-com-ubuntu-server-focal:20_04-lts"
+          NODE_AGENT_SKU_ID: "batch.node.ubuntu 20.04"
+          VM_SIZE:           "standard_a4m_v2"
+          RESOURCE_GROUP:    ${{ secrets.PRD_RESOURCE_GROUP }}
+
+
+        # The call to the az cli that actually generates the pool
+        run: |
+          az batch account login \
+          --resource-group ${{ secrets.PRD_RESOURCE_GROUP }} \
+          --name "${{ env.BATCH_ACCOUNT }}" \
+
+          az batch pool create \
+          --account-endpoint "${{ env.BATCH_ENDPOINT }}" \
+          --id "${{ env.POOL_ID }}" \
+          --image "${{ env.VM_IMAGE_TAG }}" \
+          --node-agent-sku-id "${{ env.NODE_AGENT_SKU_ID }}" \
+          --vm-size "${{ env.VM_SIZE }}" \
+
+          az batch pool autoscale enable \
+          --pool-id ${{ env.POOL_ID }} \
+          --auto-scale-formula "$(cat './batch-autoscale-formula.txt')"
+
+          # Let's get this POOL_ID var for the next step too
+          echo "POOL_ID=${{ env.POOL_ID}}" >> $GITHUB_ENV
diff --git a/.github/workflows/2_pre-Test-Model-Image-Build.yaml b/.github/workflows/2_pre-Test-Model-Image-Build.yaml
new file mode 100644
index 0000000..9a79e3d
--- /dev/null
+++ b/.github/workflows/2_pre-Test-Model-Image-Build.yaml
@@ -0,0 +1,42 @@
+name: Test Model Image Build
+run-name: (2_pre) Test Model Image - "${{ github.event.head_commit.message }}"
+
+# This GitHub Actions workflow builds a Docker image for the
+# cfa-epinow2-pipeline-docker project. In-container tests can be added here.
+
+on:
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+  schedule:
+    # Tuesdays at noon GMT time, 24 hours before the prod container is built and deployed
+    - cron: "0 12 * * 2"
+
+env:
+  # Together, these form: cfaprdbatchcr.azurecr.io/cfa-epinow2-pipeline
+  REGISTRY: cfaprdbatchcr.azurecr.io
+  IMAGE_NAME: cfa-epinow2-pipeline
+
+jobs:
+
+  _01_build-model-image:
+    runs-on: cfa-cdcgov
+    steps:
+
+      - name: Login to the Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: "cfaprdbatchcr.azurecr.io"
+          username: "cfaprdbatchcr"
+          password: ${{ secrets.CFAPRDBATCHCR_REGISTRY_PASSWORD }}
+
+      - name: Build and push model pipeline image for Azure batch
+        id: build_and_push_model_image
+        uses: docker/build-push-action@v6
+        with:
+          push: false # This can be toggled manually for tweaking.
+          tags: |
+            ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}:buildtest-latest
+            ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}:buildtest-${{ github.sha }}
+          file: ./Dockerfile
diff --git a/.github/workflows/check-news-md.yaml b/.github/workflows/3-check-news-md.yaml
similarity index 77%
rename from .github/workflows/check-news-md.yaml
rename to .github/workflows/3-check-news-md.yaml
index 07ae7de..83028a5 100644
--- a/.github/workflows/check-news-md.yaml
+++ b/.github/workflows/3-check-news-md.yaml
@@ -1,4 +1,8 @@
+# All PRs into main MUST be deliberately labelled in the NEWS.md with a succint but informative entry
+# describing the changes made - this workflow checks to make sure that this has been done.
+
 name: Check NEWS.md Update
+run-name: (3) Check News.md for Compliance - ${{ github.event.head_commit.message }} - ${{ github.ref_name }}
 
 on:
   pull_request:
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/4-R-CMD-check.yaml
similarity index 93%
rename from .github/workflows/R-CMD-check.yaml
rename to .github/workflows/4-R-CMD-check.yaml
index 0489bb7..0aac7d1 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/4-R-CMD-check.yaml
@@ -1,5 +1,9 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+name: R-CMD-check
+run-name: (4) R-CMD-check - ${{ github.event.head_commit.message }} - ${{ github.ref_name }}
+
 on:
   pull_request:
     branches: [main]
@@ -7,8 +11,6 @@ on:
     branches:
       - main
 
-name: R-CMD-check
-
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
diff --git a/.github/workflows/block-fixup.yaml b/.github/workflows/5-block-fixup.yaml
similarity index 59%
rename from .github/workflows/block-fixup.yaml
rename to .github/workflows/5-block-fixup.yaml
index b42aeb4..c88a4f5 100644
--- a/.github/workflows/block-fixup.yaml
+++ b/.github/workflows/5-block-fixup.yaml
@@ -1,4 +1,6 @@
-name: Git Checks
+name: Block Fix-up (Git Check)
+run-name: (5) Block Fix-up / Git Check - ${{ github.event.head_commit.message }} - ${{ github.ref_name }}
+
 
 on: [pull_request]
 
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/6-pkgdown.yaml
similarity index 93%
rename from .github/workflows/pkgdown.yaml
rename to .github/workflows/6-pkgdown.yaml
index a7276e8..86e18ca 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/6-pkgdown.yaml
@@ -10,6 +10,7 @@ on:
   workflow_dispatch:
 
 name: pkgdown
+run-name: (6) pkgdown - ${{ github.event.head_commit.message }} - ${{ github.ref_name }}
 
 jobs:
   pkgdown:
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/7-test-coverage.yaml
similarity index 93%
rename from .github/workflows/test-coverage.yaml
rename to .github/workflows/7-test-coverage.yaml
index e8a8471..713acd7 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/7-test-coverage.yaml
@@ -7,6 +7,7 @@ on:
     branches: [main]
 
 name: test-coverage
+run-name: (7) Test Coverage - ${{ github.event.head_commit.message }} - ${{ github.ref_name }}
 
 jobs:
   test-coverage:
@@ -27,6 +28,7 @@ jobs:
           needs: coverage
 
       - name: Test coverage
+        shell: Rscript {0}
         run: |
           covr::codecov(
             quiet = FALSE,
@@ -34,7 +36,6 @@ jobs:
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
             token = "${{ secrets.CODECOV_TOKEN }}"
           )
-        shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/8-pr-commands.yaml
similarity index 96%
rename from .github/workflows/pr-commands.yaml
rename to .github/workflows/8-pr-commands.yaml
index c9914e1..cb11c80 100644
--- a/.github/workflows/pr-commands.yaml
+++ b/.github/workflows/8-pr-commands.yaml
@@ -5,7 +5,9 @@ on:
     types: [created]
   workflow_dispatch:
 
-name: Commands
+name: PR Commands
+run-name: (8) PR Commands - ${{ github.event.head_commit.message }} - ${{ github.ref_name }}
+
 
 jobs:
   document:
diff --git a/.github/workflows/build-docker.yaml b/.github/workflows/build-docker.yaml
deleted file mode 100644
index 2cd6653..0000000
--- a/.github/workflows/build-docker.yaml
+++ /dev/null
@@ -1,73 +0,0 @@
-# This GitHub Actions workflow builds a Docker image for the
-# cfa-epinow2-pipeline-docker project. It consists of two jobs:
-# build_image_dependencies and build_image.
-#
-# - The `build_image_dependencies` job carries out the first part of a
-#   multi-stage build. It downloads and install all the dependencies
-#   listed in the `DESCRIPTION` file. It uses the `Dockerfile-dependencies`
-#   file to build the image.
-#
-#   The built image is then pushed to the corresponding registry.
-#
-#   The process is cached to avoid rebuilding the image if the dependencies
-#   have not changed. This is by hashing the `DESCRIPTION` file and the
-#   `Dockerfile-dependencies` file.
-#
-# - The build_image job builds the final image using the `Dockerfile` file.
-#   It uses the image built in the previous job as a base image.
-#
-#   During the build process, the package is installed and built. Furthermore
-#   the package is checked using `R CMD check` to ensure that it is working
-#   correctly.
-#
-#   Once the image is built, it is pushed to the corresponding registry.
-
-name: Builds Docker image
-
-on:
-  push:
-    branches:
-      - main
-  workflow_dispatch:
-
-env:
-  IMAGE_NAME: gvegayon/cfa-epinow2-pipeline
-  REGISTRY: docker.io
-
-jobs:
-  build_image_dependencies:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Check cache
-        uses: actions/cache@v3
-        id: cache
-        with:
-          key: docker-dependencies-${{ runner.os }}-${{ hashFiles('./DESCRIPTION', './Dockerfile-dependencies') }}
-          path:
-            ./DESCRIPTION
-
-      - name: Build and push
-        uses: docker/build-push-action@v6
-        if: steps.cache.outputs.cache-hit != 'true'
-        with:
-          push: false
-          tags: ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}:latest
-          file: ./Dockerfile-dependencies
-
-    outputs:
-      IMAGE_NAME: ${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}:latest
-
-  build_image:
-    needs: build_image_dependencies
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Build and push
-        uses: docker/build-push-action@v6
-        with:
-          push: false
-          tags: ${{ needs.build_image_dependencies.outputs.IMAGE_NAME }}
-          file: ./Dockerfile
diff --git a/.github/workflows/gh-act/2-dry.sh b/.github/workflows/gh-act/2-dry.sh
new file mode 100644
index 0000000..f147536
--- /dev/null
+++ b/.github/workflows/gh-act/2-dry.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# Requires that you have first run 'gh extension install nektos/gh-act'
+# as well as having installed the docker engine and added your user to the docker group
+
+# This checks syntax before you push to Github Actions, helping with debug hell
+# To run the entire pipeline locally, see 2-full.sh
+
+gh act -P cfa-cdcgov=... -n -W '.github/workflows/2-Run-Epinow2-Pipeline.yaml'
diff --git a/.github/workflows/gh-act/2-full.sh b/.github/workflows/gh-act/2-full.sh
new file mode 100644
index 0000000..cfafa9a
--- /dev/null
+++ b/.github/workflows/gh-act/2-full.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# Requires that you have first run 'gh extension install nektos/gh-act'
+# as well as having installed the docker engine and added your user to the docker group
+
+# This runs the github actions workflow locally
+
+gh act -P cfa-cdcgov=catthehacker/ubuntu:full-20.04 -W '.github/workflows/2-Run-Epinow2-Pipeline.yaml'
diff --git a/.gitignore b/.gitignore
index 2998db1..31f5dcf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -380,3 +380,7 @@ docs/site/
 # applications that require a static environment.
 #Manifest.toml
 docs
+
+# cfa-epinow2-pool-config.json
+# for now... will have to gpg encrypt
+cfa-epinow2-batch-pool-config.json
diff --git a/.secrets.baseline b/.secrets.baseline
index 63f42f9..4fc48f2 100644
--- a/.secrets.baseline
+++ b/.secrets.baseline
@@ -1,5 +1,5 @@
 {
-  "version": "1.4.0",
+  "version": "1.5.0",
   "plugins_used": [
     {
       "name": "ArtifactoryDetector"
@@ -26,6 +26,9 @@
     {
       "name": "GitHubTokenDetector"
     },
+    {
+      "name": "GitLabTokenDetector"
+    },
     {
       "name": "HexHighEntropyString",
       "limit": 3.0
@@ -36,6 +39,9 @@
     {
       "name": "IbmCosHmacDetector"
     },
+    {
+      "name": "IPPublicDetector"
+    },
     {
       "name": "JwtTokenDetector"
     },
@@ -49,9 +55,15 @@
     {
       "name": "NpmDetector"
     },
+    {
+      "name": "OpenAIDetector"
+    },
     {
       "name": "PrivateKeyDetector"
     },
+    {
+      "name": "PypiTokenDetector"
+    },
     {
       "name": "SendGridDetector"
     },
@@ -67,6 +79,9 @@
     {
       "name": "StripeDetector"
     },
+    {
+      "name": "TelegramBotTokenDetector"
+    },
     {
       "name": "TwilioKeyDetector"
     }
@@ -108,5 +123,5 @@
     }
   ],
   "results": {},
-  "generated_at": "2023-09-24T19:52:08Z"
+  "generated_at": "2024-09-20T17:50:20Z"
 }
diff --git a/Dockerfile b/Dockerfile
index 22adfd2..ac300ed 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,5 @@
-FROM gvegayon/cfa-epinow2-pipeline-dependencies:latest
+# This requires access to the Azure Container Registry
+FROM cfaprdbatchcr.azurecr.io/cfa-epinow2-pipeline-dependencies:latest
 
 # Will copy the package to the container preserving the directory structure
 COPY . pkg/
diff --git a/NEWS.md b/NEWS.md
index 821858a..5a69e5a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
 # CFAEpiNow2Pipeline (development version)
-
+* Now uses CFA Azure ACR and images in the workflows and Dockerfiles, etc.
 * Added Docker image with all the requirements to build the package.
 * Bump pre-commit hooks
 * Fix bug in warning message for incomplete data read (h/t @damonbayer)
diff --git a/batch-autoscale-formula.txt b/batch-autoscale-formula.txt
new file mode 100644
index 0000000..c98a8ee
--- /dev/null
+++ b/batch-autoscale-formula.txt
@@ -0,0 +1,20 @@
+// In this example, the pool size is adjusted based on the number of tasks in the queue.
+// Note that both comments and line breaks are acceptable in formula strings.
+
+// Get pending tasks for the past 15 minutes.
+$samples = $ActiveTasks.GetSamplePercent(TimeInterval_Minute * 15);
+
+// If we have fewer than 70 percent data points, we use the last sample point,
+// otherwise we use the maximum of last sample point and the history average.
+$tasks = $samples < 70 ? max(0, $ActiveTasks.GetSample(1)) :
+max( $ActiveTasks.GetSample(1), avg($ActiveTasks.GetSample(TimeInterval_Minute * 15)));
+
+// If number of pending tasks is not 0, set targetVM to pending tasks, otherwise half of current dedicated.
+$targetVMs = $tasks > 0 ? $tasks : max(0, $TargetDedicatedNodes / 2);
+
+// The pool size is capped at 120, if target VM value is more than that, set it to 120.
+cappedPoolSize = 120;
+$TargetDedicatedNodes = max(0, min($targetVMs, cappedPoolSize));
+
+// Set node deallocation mode - keep nodes active only until tasks finish
+$NodeDeallocationOption = taskcompletion;