diff --git a/.github/workflows/test_multiome.yml b/.github/workflows/test_multiome.yml
new file mode 100644
index 0000000000..bc1121dcc4
--- /dev/null
+++ b/.github/workflows/test_multiome.yml
@@ -0,0 +1,441 @@
+name: Test Illumina Genotyping Array
+
+# Controls when the workflow will run
+on:
+  pull_request:
+    branches: [ "develop", "staging", "master" ]
+    # Only run if files in these paths changed:
+    ####################################
+    # SET PIPELINE SPECIFIC PATHS HERE #
+    ####################################
+    paths:
+      - 'pipelines/skylab/multiome/**'
+      - 'tasks/skylab/MergeSortBam.wdl'
+      - 'tasks/skylab/FastqProcessing.wdl'
+      - 'tasks/skylab/PairedTagUtils.wdl'
+      - 'pipelines/skylab/optimus/Optimus.wdl'
+      - 'tasks/skylab/FastqProcessing.wdl'
+      - 'tasks/skylab/StarAlign.wdl'
+      - 'tasks/skylab/Metrics.wdl'
+      - 'tasks/skylab/RunEmptyDrops.wdl'
+      - 'tasks/skylab/CheckInputs.wdl'
+      - 'tasks/skylab/MergeSortBam.wdl'
+      - 'tasks/skylab/H5adUtils.wdl'
+      - 'tasks/broad/Utilities.wdl'
+      - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      - '.github/workflows/test_multiome.yml'
+      - 'verification/VerifyMultiome.wdl'
+      - 'verification/VerifyTasks.wdl'
+      - 'verification/test-wdls/TestMultiome.wdl'
+
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      useCallCache:
+        description: 'Use call cache (default: true)'
+        required: false
+        default: "true"
+      updateTruth:
+        description: 'Update truth files (default: false)'
+        required: false
+        default: "false"
+      testType:
+        description: 'Specify the type of test (Plumbing or Scientific)'
+        required: false
+      truthBranch:
+        description: 'Specify the branch for truth files (default: master)'
+        required: false
+        default: "master"
+
+env:
+  # pipeline configuration
+  PROJECT_NAME: WARP
+  PIPELINE_NAME: TestMultiome
+  DOCKSTORE_PIPELINE_NAME: Multiome
+  PIPELINE_DIR: "pipelines/skylab/multiome"
+
+  # workspace configuration
+  TESTING_WORKSPACE: WARP Tests
+  WORKSPACE_NAMESPACE: warp-pipelines
+
+  # github repo configuration
+  REPOSITORY_NAME: ${{ github.event.repository.name }}
+
+  # service account configuration
+  SA_JSON_B64: ${{ secrets.PDT_TESTER_SA_B64 }}
+  USER: pdt-tester@warp-pipeline-dev.iam.gserviceaccount.com
+
+
+jobs:
+  TestMultiome:
+    runs-on: ubuntu-latest
+    # Add "id-token" with the intended permissions.
+    permissions:
+      contents: 'read'
+      id-token: 'write'
+
+    steps:
+      # actions/checkout MUST come before auth action
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ github.ref }}
+
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          cd scripts/firecloud_api/
+          pip install -r requirements.txt
+
+      - name: Set Branch Name
+        id: set_branch
+        run: |
+          if [ -z "${{ github.head_ref }}" ]; then
+            echo "Branch name is missing, using ${GITHUB_REF##*/}"
+            echo "BRANCH_NAME=${GITHUB_REF##*/}" >> $GITHUB_ENV
+          else
+            echo "Branch name from PR: ${{ github.head_ref }}"
+            echo "BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV
+          fi
+
+      - name: Determine Github Commit Hash
+        id: determine_github_commit_hash
+        run: |
+          if [ "${{ github.event_name }}" == "workflow_dispatch" ]; then
+            echo "Using github.sha for manually triggered workflow."
+            echo "GITHUB_COMMIT_HASH=${{ github.sha }}" >> $GITHUB_ENV
+          elif [ "${{ github.event_name }}" == "pull_request" ]; then
+            echo "Using github.event.pull_request.head.sha for PR-triggered workflow."
+            echo "GITHUB_COMMIT_HASH=${{ github.event.pull_request.head.sha }}" >> $GITHUB_ENV
+          else
+            echo "Unsupported event type: ${{ github.event_name }}"
+            exit 1
+          fi
+
+      - name: Fetch Dockstore Workflow Commit Hash
+        run: |
+          # Wait 5.5 minutes for Dockstore to update
+          sleep 330
+          
+          DOCKSTORE_COMMIT_HASH_FROM_FETCH=$(python scripts/dockstore_api/fetch_dockstore_commit.py \
+            $DOCKSTORE_TOKEN \
+            $DOCKSTORE_PIPELINE_NAME \
+            $BRANCH_NAME)
+          
+          # Export the commit hash as an environment variable
+          echo "DOCKSTORE_COMMIT_HASH=$DOCKSTORE_COMMIT_HASH_FROM_FETCH" >> $GITHUB_ENV
+          echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH_FROM_FETCH"
+
+        env:
+          ## TODO NEED TO ADD DOCKSTORE_TOKEN FOR SERVICE ACCOUNT ##
+          DOCKSTORE_TOKEN: ${{ secrets.DOCKSTORE_TOKEN }}
+          DOCKSTORE_PIPELINE_NAME: ${{ env.DOCKSTORE_PIPELINE_NAME }}
+          BRANCH_NAME: ${{ env.BRANCH_NAME }}
+
+      - name: Compare Dockstore and Commit Hashes
+        id: compare_hashes
+        run: |
+          echo "Comparing hashes..."
+          echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH"
+          echo "GitHub Commit Hash: $GITHUB_COMMIT_HASH"
+
+          if [ "$DOCKSTORE_COMMIT_HASH" != "$GITHUB_COMMIT_HASH" ]; then
+            echo "Error: The Dockstore Commit Hash does not match the GitHub Commit Hash!"
+            echo "Mismatch found: $DOCKSTORE_COMMIT_HASH != $GITHUB_COMMIT_HASH"
+            exit 1
+          else
+            echo "Success: The Dockstore Commit Hash matches the GitHub Commit Hash."
+          fi
+        env:
+          DOCKSTORE_COMMIT_HASH: ${{ env.DOCKSTORE_COMMIT_HASH }}
+          GITHUB_COMMIT_HASH: ${{ env.GITHUB_COMMIT_HASH }}
+
+      - name: Set Test Type
+        id: set_test_type
+        run: |
+          if [ "${{ github.event_name }}" == "pull_request" ]; then
+            # For PRs, set based on target branch
+            if [ "${{ github.base_ref }}" == "master" ]; then
+              echo "testType=Scientific" >> $GITHUB_ENV
+              echo "testType=Scientific"
+            else
+              echo "testType=Plumbing" >> $GITHUB_ENV
+              echo "testType=Plumbing"
+            fi
+          else
+            # For workflow_dispatch, default based on target branch
+            if [ "${{ github.ref }}" == "refs/heads/master" ]; then
+              echo "testType=Scientific" >> $GITHUB_ENV
+              echo "testType is set to Scientific as the branch is ${{ github.ref }} "
+            else
+              echo "testType=Plumbing" >> $GITHUB_ENV
+              echo "testType is set to Plumbing as the branch is ${{ github.ref }}"
+            fi
+          fi
+
+      - name: Create new method configuration
+        run: |
+          echo "Creating new method configuration for branch: $BRANCH_NAME"
+
+          METHOD_CONFIG_NAME=$(python3 scripts/firecloud_api/firecloud_api.py \
+            create_new_method_config \
+            --workspace-namespace $WORKSPACE_NAMESPACE \
+            --workspace-name "$TESTING_WORKSPACE" \
+            --pipeline_name "$PIPELINE_NAME" \
+            --branch_name "$BRANCH_NAME" \
+            --sa-json-b64 "$SA_JSON_B64" \
+            --user "$USER")
+
+            echo "METHOD_CONFIG_NAME=$METHOD_CONFIG_NAME" >> $GITHUB_ENV
+        env:
+          PIPELINE_NAME: ${{ env.PIPELINE_NAME }}
+          TESTING_WORKSPACE: ${{ env.TESTING_WORKSPACE }}
+          WORKSPACE_NAMESPACE: ${{ env.WORKSPACE_NAMESPACE }}
+          USER: ${{ env.USER }}
+
+      - name: Update test inputs, Upload to Terra, Submit, Monitor and Retrieve Outputs
+        run: |
+          UPDATE_TRUTH="${{ github.event.inputs.updateTruth || 'false' }}"
+          USE_CALL_CACHE="${{ github.event.inputs.useCallCache || 'true' }}"
+          TRUTH_BRANCH="${{ github.event.inputs.truthBranch || 'master' }}"
+          CURRENT_TIME=$(date +"%Y-%m-%d-%H-%M-%S")
+          MAX_RETRIES=2
+          RETRY_DELAY=300  # 300 seconds = 5 minutes
+          # Initialize variables to aggregate statuses and outputs
+          ALL_WORKFLOW_STATUSES="Workflow ID | Status"$'\n'"--- | ---"
+          ALL_OUTPUTS=""
+          # Initialize arrays to track submission and workflow statuses
+          declare -a SUBMISSION_IDS
+          declare -A WORKFLOW_STATUSES
+          OVERALL_SUCCESS=true  
+
+          # Convert UPDATE_TRUTH and USE_CALL_CACHE to a boolean-friendly format ("true" -> true, "false" -> false)
+          if [ "$UPDATE_TRUTH" = "true" ]; then
+              UPDATE_TRUTH_BOOL=true
+          else
+              UPDATE_TRUTH_BOOL=false
+          fi
+
+          if [ "$USE_CALL_CACHE" == "true" ]; then
+              USE_CALL_CACHE_BOOL=true
+          else
+              USE_CALL_CACHE_BOOL=false
+          fi
+
+          TEST_TYPE="${{ env.testType }}"
+          INPUTS_DIR="$PIPELINE_DIR/test_inputs/$TEST_TYPE"
+          echo "Running tests with test type: $TEST_TYPE"
+
+          TRUTH_PATH="gs://broad-gotc-test-storage/$DOCKSTORE_PIPELINE_NAME/truth/$(echo "$TEST_TYPE" | tr '[:upper:]' '[:lower:]')/$TRUTH_BRANCH"
+          echo "Truth path: $TRUTH_PATH"
+          RESULTS_PATH="gs://broad-gotc-test-storage/$DOCKSTORE_PIPELINE_NAME/results/$CURRENT_TIME"
+          
+          
+          
+          # 1. Submit all jobs first and store their submission IDs
+          for input_file in "$INPUTS_DIR"/*.json; do
+            test_input_file=$(python3 scripts/firecloud_api/UpdateTestInputs.py --truth_path "$TRUTH_PATH" \
+                --results_path "$RESULTS_PATH" \
+                --inputs_json "$input_file" \
+                --update_truth "$UPDATE_TRUTH_BOOL" \
+                --branch_name "$BRANCH_NAME" )
+            echo "Uploading the test input file: $test_input_file"
+
+            # Create the submission_data.json file for this input_file
+            input_file_filename=$(basename $input_file)
+            SUBMISSION_DATA_FILE="submission_data.json"
+            printf '{
+              "methodConfigurationNamespace": "%s",
+              "methodConfigurationName": "%s",
+              "useCallCache": %s,
+              "deleteIntermediateOutputFiles": false,
+              "useReferenceDisks": true,
+              "memoryRetryMultiplier": 1.2,
+              "workflowFailureMode": "NoNewCalls",
+              "userComment": "%s",
+              "ignoreEmptyOutputs": false
+            }' "$WORKSPACE_NAMESPACE" "$METHOD_CONFIG_NAME" "$USE_CALL_CACHE_BOOL" "$input_file_filename" > "$SUBMISSION_DATA_FILE"
+          
+            echo "Created submission data file: $SUBMISSION_DATA_FILE"
+            cat "$SUBMISSION_DATA_FILE"
+
+            # Upload test input file
+            python3 scripts/firecloud_api/firecloud_api.py \
+                upload_test_inputs \
+                --workspace-namespace $WORKSPACE_NAMESPACE \
+                --workspace-name "$TESTING_WORKSPACE" \
+                --pipeline_name "$PIPELINE_NAME" \
+                --test_input_file "$test_input_file" \
+                --branch_name "$BRANCH_NAME" \
+                --sa-json-b64 "$SA_JSON_B64" \
+                --user "$USER"
+
+            attempt=1
+            while [ $attempt -le $MAX_RETRIES ]; do
+              SUBMISSION_ID=$(python3 scripts/firecloud_api/firecloud_api.py submit_job \
+               --workspace-namespace "$WORKSPACE_NAMESPACE" \
+               --workspace-name "$TESTING_WORKSPACE" \
+               --sa-json-b64 "$SA_JSON_B64" \
+               --user "$USER" \
+               --submission_data_file "$SUBMISSION_DATA_FILE")
+
+              echo "Submission ID: $SUBMISSION_ID"
+
+              if [[ "$SUBMISSION_ID" == *"404"* || -z "$SUBMISSION_ID" ]]; then
+                  echo "Error in submission, retrying in $RETRY_DELAY seconds..."
+                  ((attempt++))
+                  if [ $attempt -gt $MAX_RETRIES ]; then
+                      echo "Max retries reached. Exiting..."
+                      exit 1
+                  fi
+                  sleep $RETRY_DELAY
+                  continue
+              fi
+
+              echo "Submission successful. Submission ID: $SUBMISSION_ID"
+              SUBMISSION_IDS+=("$SUBMISSION_ID")
+              break
+            done
+          done
+
+          echo "All jobs have been submitted. Starting to poll for statuses..."
+
+          # Continue with polling and output retrieval...
+          
+          # 2. After all submissions are done, start polling for statuses of all jobs
+          for SUBMISSION_ID in "${SUBMISSION_IDS[@]}"; do
+            attempt=1
+            while [ $attempt -le $MAX_RETRIES ]; do
+              echo "Polling for Submission ID: $SUBMISSION_ID"
+              RESPONSE=$(python3 scripts/firecloud_api/firecloud_api.py poll_job_status \
+                  --submission_id "$SUBMISSION_ID" \
+                  --sa-json-b64 "$SA_JSON_B64" \
+                  --user "$USER" \
+                  --workspace-namespace "$WORKSPACE_NAMESPACE" \
+                  --workspace-name "$TESTING_WORKSPACE")
+          
+              if [ -z "$RESPONSE" ]; then
+                  echo "Failed to retrieve Workflow IDs for submission: $SUBMISSION_ID"
+                  OVERALL_SUCCESS=false
+                  ((attempt++))
+                  if [ $attempt -gt $MAX_RETRIES ]; then
+                      echo "Max retries reached. Exiting..."
+                      exit 1
+                  fi
+                  sleep $RETRY_DELAY
+                  continue
+              fi
+          
+              WORKFLOW_STATUSES_FOR_SUBMISSION=$(echo "$RESPONSE" | jq -r 'to_entries | map(.key + " | " + .value) | .[]')
+              WORKFLOW_STATUSES["$SUBMISSION_ID"]="$WORKFLOW_STATUSES_FOR_SUBMISSION"
+          
+              # Check if any workflow failed or errored
+              FAILED_WORKFLOWS=$(echo "$RESPONSE" | jq -r 'to_entries | .[] | select(.value == "Failed" or .value == "Aborted" or .value == "Aborting") | .key')
+              if [ ! -z "$FAILED_WORKFLOWS" ]; then
+                  echo "Failed workflows detected:"
+                  echo "$FAILED_WORKFLOWS"
+                  OVERALL_SUCCESS=false
+              fi
+          
+              # retrieve workflow outputs
+              echo "Retrieving workflow outputs for Submission ID: $SUBMISSION_ID..."
+              for WORKFLOW_ID in $(echo "$RESPONSE" | jq -r 'keys[]'); do
+                   WORKFLOW_OUTPUT=$(python3 scripts/firecloud_api/firecloud_api.py get_workflow_outputs \
+                    --user "$USER" \
+                    --sa-json-b64 "$SA_JSON_B64" \
+                    --submission_id "$SUBMISSION_ID" \
+                    --workspace-namespace $WORKSPACE_NAMESPACE \
+                    --workspace-name "$TESTING_WORKSPACE" \
+                    --workflow_id "$WORKFLOW_ID" \
+                    --pipeline_name "$PIPELINE_NAME")
+                    ALL_OUTPUTS+="$WORKFLOW_OUTPUT"$'\n'
+              done
+              break
+            done
+          done
+          
+          # Generate the final summary after all processing is complete
+          FINAL_SUMMARY="## Combined Workflow Statuses\n\n"
+          
+          # Add all workflow statuses to the summary
+          for SUBMISSION_ID in "${!WORKFLOW_STATUSES[@]}"; do
+            # Generate the Terra URL for the submission
+            SUBMISSION_URL="https://app.terra.bio/#workspaces/$WORKSPACE_NAMESPACE/WARP%20Tests/job_history/$SUBMISSION_ID"
+
+            # Add the Submission ID as a hyperlink
+            FINAL_SUMMARY+="[Submission ID: $SUBMISSION_ID]($SUBMISSION_URL)\n"
+
+            # Add the workflows and statuses for this submission
+            FINAL_SUMMARY+="${WORKFLOW_STATUSES[$SUBMISSION_ID]}\n\n"
+          done
+          
+          # Write the complete summary once at the end
+          echo -e "$FINAL_SUMMARY" >> $GITHUB_STEP_SUMMARY
+          
+          # Exit with error if any workflows failed
+          if [ "$OVERALL_SUCCESS" = false ]; then          
+              echo ""
+              echo ""
+              echo "****************************************************************************************"
+              echo "****************************************************************************************"
+              echo ""
+              echo "One or more workflows failed in Terra. Check the workflow status summary for details."
+              echo ""
+              echo "****************************************************************************************"
+              echo "****************************************************************************************"
+              echo ""
+              echo ""
+              exit 1
+          fi
+        env:
+          PIPELINE_NAME: ${{ env.PIPELINE_NAME }}
+          TESTING_WORKSPACE: ${{ env.TESTING_WORKSPACE }}
+          METHOD_CONFIG_NAME: ${{ env.METHOD_CONFIG_NAME }}
+          WORKSPACE_NAMESPACE: ${{ env.WORKSPACE_NAMESPACE }}
+          USER: ${{ env.USER }}
+          DOCKSTORE_PIPELINE_NAME: ${{ env.DOCKSTORE_PIPELINE_NAME }}
+          PIPELINE_DIR: ${{ env.PIPELINE_DIR }}
+
+      - name: Delete Method Configuration
+        if: always() # Ensures it runs regardless of success or failure
+        run: |
+          echo "Deleting method configuration for branch: $BRANCH_NAME"
+          DELETE_RESPONSE=$(python3 scripts/firecloud_api/firecloud_api.py delete_method_config \
+            --workspace-namespace $WORKSPACE_NAMESPACE \
+            --workspace-name "$TESTING_WORKSPACE" \
+            --pipeline_name "$PIPELINE_NAME" \
+            --branch_name "$BRANCH_NAME" \
+            --sa-json-b64 "$SA_JSON_B64" \
+            --user "$USER" \
+            --method_config_name "$METHOD_CONFIG_NAME")
+            echo "Delete response: $DELETE_RESPONSE"
+          if [ "$DELETE_RESPONSE" == "True" ]; then
+            echo "Method configuration deleted successfully."
+          else
+            echo "Error: Method configuration deletion failed."
+            exit 1
+          fi
+
+        env:
+          PIPELINE_NAME: ${{ env.PIPELINE_NAME }}
+          BRANCH_NAME: ${{ env.BRANCH_NAME }}
+          SA_JSON_B64: ${{ secrets.PDT_TESTER_SA_B64 }}
+          METHOD_CONFIG_NAME: ${{ env.METHOD_CONFIG_NAME }}
+          WORKSPACE_NAMESPACE: ${{ env.WORKSPACE_NAMESPACE }}
+          TESTING_WORKSPACE: ${{ env.TESTING_WORKSPACE }}
+          USER: ${{ env.USER }}
+
+      - name: Print Summary on Success
+        if: success()
+        run: |
+          echo "# :white_check_mark: Pipeline Execution Summary :white_check_mark:" >> $GITHUB_STEP_SUMMARY
+
+      - name: Print Summary on Failure
+        if: failure()
+        run: |
+          echo "# :x: Pipeline Execution Summary (on Failure) :x: " >> $GITHUB_STEP_SUMMARY
\ No newline at end of file
diff --git a/verification/test-wdls/TestMultiome.wdl b/verification/test-wdls/TestMultiome.wdl
index 10197b4237..00df0dd856 100644
--- a/verification/test-wdls/TestMultiome.wdl
+++ b/verification/test-wdls/TestMultiome.wdl
@@ -4,7 +4,7 @@ version 1.0
 import "../../pipelines/skylab/multiome/Multiome.wdl" as Multiome
 import "../../verification/VerifyMultiome.wdl" as VerifyMultiome
 import "../../tasks/broad/Utilities.wdl" as Utilities
-import "../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy
+import "../../tasks/broad/TerraCopyFilesFromCloudToCloud.wdl" as Copy
 
 
 workflow TestMultiome {
@@ -50,8 +50,6 @@ workflow TestMultiome {
       String truth_path
       String results_path
       Boolean update_truth
-      String vault_token_path
-      String google_account_vault_path
       Boolean run_cellbender = false
 
     }
@@ -123,21 +121,17 @@ workflow TestMultiome {
     ])
 
     # Copy results of pipeline to test results bucket
-    call Copy.CopyFilesFromCloudToCloud as CopyToTestResults {
+    call Copy.TerraCopyFilesFromCloudToCloud as CopyToTestResults {
       input:
         files_to_copy             = flatten([pipeline_outputs, pipeline_metrics]),
-        vault_token_path          = vault_token_path,
-        google_account_vault_path = google_account_vault_path,
         destination_cloud_path    = results_path
     }
   
     # If updating truth then copy output to truth bucket
     if (update_truth){
-      call Copy.CopyFilesFromCloudToCloud as CopyToTruth {
+      call Copy.TerraCopyFilesFromCloudToCloud as CopyToTruth {
         input: 
           files_to_copy             = flatten([pipeline_outputs, pipeline_metrics]),
-          vault_token_path          = vault_token_path,
-          google_account_vault_path = google_account_vault_path,
           destination_cloud_path    = truth_path
       }
     }