diff --git a/.github/workflows/build-push-dev-image.yml b/.github/workflows/build-push-dev-image.yml
new file mode 100644
index 00000000..13f8cfb7
--- /dev/null
+++ b/.github/workflows/build-push-dev-image.yml
@@ -0,0 +1,86 @@
+# Workflow responsible for the 
+# development release processes.
+#
+name: Build-Push-Dev-Image
+on:
+  push:
+    branches:
+      - develop
+    paths-ignore:
+      - README.md
+      - .old_cicd/*
+      - .github/*
+      - .github/workflows/*
+      - LICENSE
+      - .gitignore
+      - .dockerignore
+      - .githooks
+  # Do not build another image on a pull request.
+  # Any push to develop will trigger a new build however.
+  pull_request:
+    branches-ignore:
+      - '*'
+
+jobs:
+  build-push-dev-image:
+    runs-on: ubuntu-latest
+    steps:
+    
+    - name: Checkout Code
+      uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }} 
+        # fetch-depth: 0 means, get all branches and commits
+        fetch-depth: 0
+
+    - name: Set short git commit SHA
+      id: vars
+      run: |
+        echo "short_sha=$(git rev-parse --short ${{ github.sha }})" >> $GITHUB_OUTPUT
+    # https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
+
+    - name: Confirm git commit SHA output
+      run: echo ${{ steps.vars.outputs.short_sha }}
+
+    # Docker Buildx is important to caching in the Build And Push Container
+    # step
+    # https://github.com/marketplace/actions/build-and-push-docker-images
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+      with:
+        driver-opts: |
+          network=host
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        logout: true
+
+    - name: Login to Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: containers.renci.org
+        username: ${{ secrets.CONTAINERHUB_USERNAME }}
+        password: ${{ secrets.CONTAINERHUB_TOKEN }}
+        logout: true
+
+
+    # Notes on Cache: 
+    # https://docs.docker.com/build/ci/github-actions/examples/#inline-cache
+    - name: Build Push Container
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: true
+        # Push to renci-registry and dockerhub here.
+        # cache comes from dockerhub.
+        tags: |
+          ${{ github.repository }}:develop
+          ${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+          containers.renci.org/${{ github.repository }}:develop
+          containers.renci.org/${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+        cache-from: type=registry,ref=${{ github.repository }}:buildcache-dev
+        cache-to: type=registry,ref=${{ github.repository }}:buildcache-dev,mode=max
\ No newline at end of file
diff --git a/.github/workflows/build-push-release.yml b/.github/workflows/build-push-release.yml
new file mode 100644
index 00000000..07b22d21
--- /dev/null
+++ b/.github/workflows/build-push-release.yml
@@ -0,0 +1,131 @@
+# Workflow responsible for the 
+# major release processes.
+#
+
+name: Build-Push-Release
+on:
+  push:
+    branches:
+      - master 
+      - main
+    paths-ignore:
+      - README.md
+      - .old_cicd/*
+      - .github/*
+      - .github/workflows/*
+      - LICENSE
+      - .gitignore
+      - .dockerignore
+      - .githooks
+    tags-ignore:
+      - '*'
+jobs:
+  build-push-release:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Code
+      uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }} 
+        fetch-depth: 0
+
+    - name: Set short git commit SHA
+      id: vars
+      run: |
+        echo "short_sha=$(git rev-parse --short ${{ github.sha }})" >> $GITHUB_OUTPUT
+    # https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
+
+    - name: Confirm git commit SHA output
+      run: echo ${{ steps.vars.outputs.short_sha }}
+
+    # https://github.com/marketplace/actions/git-semantic-version
+    - name: Semver Check
+      uses: paulhatch/semantic-version@v5.0.3
+      id: version
+      with:
+        # The prefix to use to identify tags
+        tag_prefix: "v"
+        # A string which, if present in a git commit, indicates that a change represents a
+        # major (breaking) change, supports regular expressions wrapped with '/'
+        major_pattern: "/breaking:|major:/"
+        # A string which indicates the flags used by the `major_pattern` regular expression. Supported flags: idgs
+        major_regexp_flags: "ig"
+        # Same as above except indicating a minor change, supports regular expressions wrapped with '/'
+        minor_pattern: "/feat:|feature:|minor:/"
+        # A string which indicates the flags used by the `minor_pattern` regular expression. Supported flags: idgs
+        minor_regexp_flags: "ig"
+        # A string to determine the format of the version output
+        # version_format: "${major}.${minor}.${patch}-prerelease${increment}"
+        version_format: "${major}.${minor}.${patch}"
+        search_commit_body: false
+
+    # Docker Buildx is important to caching in the Build And Push Container
+    # step
+    # https://github.com/marketplace/actions/build-and-push-docker-images
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+      with:
+        driver-opts: |
+          network=host
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        logout: true
+
+    - name: Login to Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: containers.renci.org
+        username: ${{ secrets.CONTAINERHUB_USERNAME }}
+        password: ${{ secrets.CONTAINERHUB_TOKEN }}
+        logout: true
+
+    # Notes on Cache: 
+    # https://docs.docker.com/build/ci/github-actions/examples/#inline-cache
+    - name: Build Push Container
+      uses: docker/build-push-action@v5
+      with:
+        push: true
+        # Push to renci-registry and dockerhub here.
+        # cache comes from dockerhub.
+        tags: |
+          containers.renci.org/${{ github.repository }}:v${{ steps.version.outputs.version }}
+          containers.renci.org/${{ github.repository }}:latest
+          containers.renci.org/${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+          ${{ github.repository }}:v${{ steps.version.outputs.version }}
+          ${{ github.repository }}:latest
+          ${{ github.repository }}:${{ steps.vars.outputs.short_sha }}
+        cache-from: type=registry,ref=${{ github.repository }}:buildcache-release
+        cache-to: type=registry,ref=${{ github.repository }}:buildcache-release,mode=max
+
+#==========================TAG & RELEASE W/ NOTES =========================
+
+    # Note: GITHUB_TOKEN is autogenerated feature of github app
+    # which is auto-enabled when using github actions.
+    # https://docs.github.com/en/actions/security-guides/automatic-token-authentication
+    # https://docs.github.com/en/rest/git/tags?apiVersion=2022-11-28#create-a-tag-object
+    # https://docs.github.com/en/rest/git/refs?apiVersion=2022-11-28#create-a-reference
+    # This creates a "lightweight" ref tag.
+    - name: Create Tag for Release
+      run: |
+        curl \
+        -s --fail -X POST \
+        -H "Accept: application/vnd.github+json" \
+        -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+        -H "X-GitHub-Api-Version: 2022-11-28" \
+        https://api.github.com/repos/${{ github.repository }}/git/refs \
+        -d '{"ref":"refs/tags/v${{ steps.version.outputs.version }}","sha":"${{ github.sha }}"}'
+        
+#   https://cli.github.com/manual/gh_release_create
+    - name: Create Release
+      env:
+        RELEASE_VERSION: ${{ steps.version.outputs.version }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        gh release create ${{ env.RELEASE_VERSION }} \
+          -t "${{ env.RELEASE_VERSION }}" \
+          --generate-notes \
+          --latest
\ No newline at end of file
diff --git a/.github/workflows/code-checks.yml b/.github/workflows/code-checks.yml
new file mode 100644
index 00000000..b7f3e6a5
--- /dev/null
+++ b/.github/workflows/code-checks.yml
@@ -0,0 +1,129 @@
+# Workflow responsible for core acceptance testing.
+# Tests Currently Run:
+#     - flake8-linter
+#     - PYTest
+#     - Bandit
+# For PR Vulnerability Scanning a separate workflow will run.
+# The build-push-dev-image and build-push-release workflows
+# handle the develop and release image storage respectively.
+#
+#
+
+name: Code-Checks
+on:
+  push:
+    branches-ignore:
+      - master
+      - main
+      - develop
+  pull_request:
+    branches:
+      - develop
+      - master
+      - main
+    types: [opened, synchronize]
+    paths-ignore:
+      - README.md
+      - .old_cicd/*
+      - .github/*
+      - .github/workflows/*
+      - LICENSE
+      - .gitignore
+      - .dockerignore
+      - .githooks
+
+jobs:
+  ############################## flake8-linter ##############################
+  flake8-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      # Currently actions/setup-python supports caching
+      # but the cache is not as robust as cache action.
+      # Here we cache the entire python env which speeds subsequent builds up alot. (alot being scientific term)
+      # Ref: https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
+      - uses: actions/cache@v3
+        name: Cache Python
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Install Requirements
+        run: |
+          pip install -r requirements.txt
+
+      - name: Lint with flake8
+        run: |
+          pip install flake8
+          flake8 --ignore=E,W dags
+        # We continue on error here until the code is clean
+        # flake8 --ignore=E,W --exit-zero .
+        continue-on-error: true
+
+  ################################### PYTEST ###################################
+  # pytest:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #   - uses: actions/checkout@v3
+  #   - name: Set up Python
+  #     uses: actions/setup-python@v4
+  #     with:
+  #       python-version: '3.12'
+
+  #   - name: Install Requirements
+  #     run: |
+  #       pip install -r requirements.txt
+  #       pip install coverage
+  #       pip install ./tests
+
+  #   - name: Test with pytest
+  #     run: |
+  #       make test
+  ############################## test-image-build ##############################
+  test-image-build:
+    runs-on: ubuntu-latest
+    # if: ${{ github.actor == 'dependabot[bot]' }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set short git commit SHA
+        id: vars
+        run: |
+          echo "short_sha=$(git rev-parse --short ${{ github.sha }})" >> $GITHUB_OUTPUT
+      # https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
+      - name: Confirm git commit SHA output
+        run: echo ${{ steps.vars.outputs.short_sha }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          logout: true
+
+      - name: Parse Github Reference Name
+        id: branch
+        run: |
+          REF=${{ github.ref_name }}
+          echo "GHR=${REF%/*}" >> $GITHUB_OUTPUT
+
+      # Notes on Cache:
+      # https://docs.docker.com/build/ci/github-actions/examples/#inline-cache
+      - name: Build Container
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: |
+            ${{ github.repository }}:test_${{ steps.branch.outputs.GHR }}
+          cache-from: type=registry,ref=${{ github.repository }}:buildcache
+          cache-to: type=registry,ref=${{ github.repository }}:buildcache,mode=max
diff --git a/.github/workflows/trivy-pr-scan.yml b/.github/workflows/trivy-pr-scan.yml
new file mode 100644
index 00000000..1e7bc060
--- /dev/null
+++ b/.github/workflows/trivy-pr-scan.yml
@@ -0,0 +1,67 @@
+name: trivy-pr-scan 
+on:
+  pull_request:
+    branches:
+      - develop
+      - master
+      - main 
+    types: [ opened, synchronize ]
+    paths-ignore:
+    - README.md
+    - .old_cicd/*
+    - .github/*
+    - .github/workflows/*
+    - LICENSE
+    - .gitignore
+    - .dockerignore
+    - .githooks
+
+jobs:
+ trivy-pr-scan:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+      with:
+        driver-opts: |
+          network=host
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        logout: true
+
+    # Notes on Cache: 
+    # https://docs.docker.com/build/ci/github-actions/examples/#inline-cache
+    - name: Build Container
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: false
+        load: true
+        tags: ${{ github.repository }}:vuln-test
+        cache-from: type=registry,ref=${{ github.repository }}:buildcache
+        cache-to: type=registry,ref=${{ github.repository }}:buildcache,mode=max
+
+    # We will not be concerned with Medium and Low vulnerabilities
+    - name: Run Trivy vulnerability scanner
+      uses: aquasecurity/trivy-action@master
+      with:
+        image-ref: '${{ github.repository }}:vuln-test'
+        format: 'sarif'
+        severity: 'CRITICAL,HIGH'
+        ignore-unfixed: true
+        output: 'trivy-results.sarif'
+        exit-code: '1'
+    # Scan results should be viewable in GitHub Security Dashboard
+    # We still fail the job if results are found, so below will always run
+    # unless manually canceled.
+    - name: Upload Trivy scan results to GitHub Security tab
+      uses: github/codeql-action/upload-sarif@v2
+      if: '!cancelled()'
+      with:
+        sarif_file: 'trivy-results.sarif'
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index 49c1fd26..7760c983 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,7 +2,7 @@ FROM apache/airflow:2.7.2-python3.11
 
 USER root
 RUN apt-get update && \
-    apt-get install -y git nano vim 
+    apt-get install -y git nano vim gcc
 COPY requirements.txt requirements.txt
 USER airflow
 RUN pip install -r requirements.txt
diff --git a/Jenkinsfile b/Jenkinsfile
deleted file mode 100644
index a68ba92b..00000000
--- a/Jenkinsfile
+++ /dev/null
@@ -1,84 +0,0 @@
-library 'pipeline-utils@master'
-
-pipeline {
-    agent {
-        kubernetes {
-            label 'kaniko-build-agent'
-            yaml '''
-kind: Pod
-metadata:
-  name: kaniko
-spec:
-  containers:
-  - name: jnlp
-    workingDir: /home/jenkins/agent
-  - name: kaniko
-    workingDir: /home/jenkins/agent
-    image: gcr.io/kaniko-project/executor:debug
-    imagePullPolicy: Always
-    resources:
-      requests:
-        cpu: "512m"
-        memory: "1024Mi"
-        ephemeral-storage: "4Gi"
-      limits:
-        cpu: "1024m"
-        memory: "2048Mi"
-        ephemeral-storage: "8Gi"
-    command:
-    - /busybox/cat
-    tty: true
-    volumeMounts:
-    - name: jenkins-docker-cfg
-      mountPath: /kaniko/.docker
-  volumes:
-  - name: jenkins-docker-cfg
-    projected:
-      sources:
-      - secret:
-          name: rencibuild-imagepull-secret
-          items:
-            - key: .dockerconfigjson
-              path: config.json
-'''
-        }
-    }
-    environment {
-        PATH = "/busybox:/kaniko:/ko-app/:$PATH"
-        DOCKERHUB_CREDS = credentials("${env.CONTAINERS_REGISTRY_CREDS_ID_STR}")
-        REGISTRY = "${env.REGISTRY}"
-        REG_OWNER="helxplatform"
-        REG_APP="roger"
-        COMMIT_HASH="${sh(script:"git rev-parse --short HEAD", returnStdout: true).trim()}"
-        VERSION_FILE="./dags/_version.py"
-        VERSION="${sh(script:'awk \'{ print $3 }\' ./dags/_version.py | xargs', returnStdout: true).trim()}"
-        IMAGE_NAME="${REGISTRY}/${REG_OWNER}/${REG_APP}"
-        TAG1="$BRANCH_NAME"
-        TAG2="$COMMIT_HASH"
-        TAG3="$VERSION"
-        TAG4="latest"
-    }
-    stages {
-        stage('Test') {
-            steps {
-                sh '''
-                echo "Test stage"
-                '''
-            }
-        }
-        stage('Build') {
-            steps {
-                script {
-                    container(name: 'kaniko', shell: '/busybox/sh') {
-                        if (env.BRANCH_NAME == "main") {
-                          // Tag with latest and version iff when pushed to master
-                          kaniko.buildAndPush("./Dockerfile", ["$IMAGE_NAME:$TAG1", "$IMAGE_NAME:$TAG2", "$IMAGE_NAME:$TAG3", "$IMAGE_NAME:$TAG4"])
-                        } else {
-                          kaniko.buildAndPush("./Dockerfile", ["$IMAGE_NAME:$TAG1", "$IMAGE_NAME:$TAG2"])
-                        }
-                    }
-                }
-            }          
-        }        
-    }
-}
diff --git a/dags/roger/config/__init__.py b/dags/roger/config/__init__.py
index ac9eb23a..71111f39 100644
--- a/dags/roger/config/__init__.py
+++ b/dags/roger/config/__init__.py
@@ -99,6 +99,21 @@ class AnnotationConfig(DictLike):
             "sapbert": {
                 "classification_url": "https://med-nemo.apps.renci.org/annotate/",
                 "annotator_url": "https://babel-sapbert.apps.renci.org/annotate/",
+                "score_threshold": 0.8,
+                "bagel": {
+                    "enabled": False,
+                    "url": "https://bagel.apps.renci.org/group_synonyms_openai",
+                    "prompt": "bagel/ask_classes",
+                    "llm_args": {
+                        "llm_model_name": "gpt-4o-2024-05-13",
+                        "organization": "",
+                        "access_key": "",
+                        "llm_model_args": {
+                            "top_p": 0,
+                            "temperature": 0.1
+                        }
+                    }
+                }
             },
         }
     )
@@ -119,6 +134,9 @@ class AnnotationConfig(DictLike):
         "PATO", "CHEBI", "MONDO", "UBERON", "HP", "MESH", "UMLS"
     ])
 
+    def __post_init__(self):
+        self.annotator_args["sapbert"]["bagel"]["enabled"] = self.annotator_args["sapbert"]["bagel"][
+                                                                 "enabled"].lower() == "true"
 
 
 @dataclass
diff --git a/dags/roger/config/config.yaml b/dags/roger/config/config.yaml
index e9402ce4..c407555f 100644
--- a/dags/roger/config/config.yaml
+++ b/dags/roger/config/config.yaml
@@ -1,6 +1,6 @@
 redisgraph:
   username: ""
-  password: "12345"
+  password: "weak"
   host: localhost
   graph: test
   port: 6379
@@ -42,13 +42,25 @@ bulk_loader:
 
 annotation:
   clear_http_cache: false
-  annotator_type: monarch
+  annotator_type: sapbert
   annotator_args:
     monarch:
       url: "https://api.monarchinitiative.org/api/nlp/annotate/entities?min_length=4&longest_only=false&include_abbreviation=false&include_acronym=false&include_numbers=false&content="
     sapbert: 
       classification_url: "https://med-nemo.apps.renci.org/annotate/"
-      annotator_url: "https://babel-sapbert.apps.renci.org/annotate/"
+      annotator_url: "https://sap-qdrant.apps.renci.org/annotate/"
+      score_threshold: 0.8
+      bagel:
+        enabled: false
+        url: "http://localhost:9099/group_synonyms_openai"
+        prompt: "bagel/ask_classes"
+        llm_args:
+          llm_model_name: "gpt-4o-2024-05-13"
+          organization:
+          access_key:
+          llm_model_args:
+            top_p: 0
+            temperature: 0.1
   normalizer: "https://nodenormalization-dev.apps.renci.org/get_normalized_nodes?conflate=false&description=true&curie="
   synonym_service: "https://name-resolution-sri.renci.org/reverse_lookup"
   ontology_metadata: "https://api.monarchinitiative.org/api/bioentity/"
@@ -93,9 +105,9 @@ indexing:
         action: "files"
 
 elasticsearch:
-  host: elasticsearch
+  host: localhost
   username: elastic
-  password: ""
+  password: "12345"
   nboost_host: ""
   scheme: "http"
   ca_path: ""
diff --git a/dags/roger/pipelines/bdc_pipelines.py b/dags/roger/pipelines/bdc_pipelines.py
new file mode 100644
index 00000000..5a945641
--- /dev/null
+++ b/dags/roger/pipelines/bdc_pipelines.py
@@ -0,0 +1,48 @@
+"Dug pipeline for dbGaP data set"
+
+from roger.pipelines import DugPipeline
+
+class BIOLINCCdbGaPPipeline(DugPipeline):
+    "Pipeline for the dbGaP data set"
+    pipeline_name = 'biolincc'
+    parser_name = 'biolincc'
+
+
+class covid19dbGaPPipeline(DugPipeline):
+    "Pipeline for the dbGaP data set"
+    pipeline_name = 'covid19-dbgap'
+    parser_name = 'covid19'
+
+class dirDbGaPPipeline(DugPipeline):
+    pipeline_name = "dir-dbgap"
+    parser_name = "dir"
+
+class LungMapDbGaPPipeline(DugPipeline):
+    pipeline_name = "lungmap-dbgap"
+    parser_name = "lungmap"
+
+class nsrrDbGaPPipeline(DugPipeline):
+    pipeline_name = "nsrr-dbgap"
+    parser_name = "nsrr"
+
+class ParentDbGaPPipeline(DugPipeline):
+    pipeline_name = "parent-dbgap"
+    parser_name = "parent"
+
+class PCGCDbGaPPipeline(DugPipeline):
+    pipeline_name = "pcgc-dbgap"
+    parser_name = "pcgc"
+
+class RecoverDbGaPPipeline(DugPipeline):
+    pipeline_name = "recover-dbgap"
+    parser_name = "recover"
+
+class TopmedDBGaPPipeline(DugPipeline):
+    pipeline_name = "topmed-gen3-dbgap"
+    parser_name = "topmeddbgap"
+
+class CureSCPipeline(DugPipeline):
+    pipeline_name = "curesc-dbgap"
+    parser_name = "curesc"
+
+
diff --git a/requirements.txt b/requirements.txt
index d1b1f68f..3a0ee223 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,7 +6,7 @@ jsonpickle
 redisgraph-bulk-loader==0.12.3
 pytest
 PyYAML
-git+https://github.com/helxplatform/dug@2.13.1
+git+https://github.com/helxplatform/dug@2.13.2
 orjson
 kg-utils==0.0.6
 bmt==1.1.0