diff --git a/.github/workflows/test_illumina_genotyping_array.yml b/.github/workflows/test_illumina_genotyping_array.yml
index a0ca0b0441..b28a917966 100644
--- a/.github/workflows/test_illumina_genotyping_array.yml
+++ b/.github/workflows/test_illumina_genotyping_array.yml
@@ -134,17 +134,32 @@ jobs:
       - name: Update test inputs and Upload to Terra
         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
           
-          # Convert UPDATE_TRUTH to a boolean-friendly format ("true" -> true, "false" -> false)
+          
+          # 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 [ "$USE_CALL_CACHE" == "true" ]; then
+              USE_CALL_CACHE_BOOL=true
+          else
+              USE_CALL_CACHE_BOOL=false
+          fi
+          
           PIPELINE_NAME="TestIlluminaGenotypingArray"
           PIPELINE_DIR="pipelines/broad/genotyping/illumina"
           TEST_TYPE="${{ env.testType }}"
@@ -156,14 +171,14 @@ jobs:
           RESULTS_PATH="gs://broad-gotc-test-storage/IlluminaGenotypingArray/results/$CURRENT_TIME"
           
           for input_file in "$INPUTS_DIR"/*.json; do
-             echo "Processing input file: $input_file"
-             test_input_file=$(python3 scripts/firecloud_api/UpdateTestInputs.py --truth_path "$TRUTH_PATH" \
-                 --results_path "$RESULTS_PATH" \
-                 --inputs_json "$input_file" \
-                 --update_truth "$UPDATE_TRUTH_BOOL" \
-                 --commit_hash "$COMMIT_HASH" )
-             echo "Uploading the test input file: $test_input_file"
-             echo "Branch name: $branch_name"
+            echo "Processing input file: $input_file"
+            test_input_file=$(python3 scripts/firecloud_api/UpdateTestInputs.py --truth_path "$TRUTH_PATH" \
+                --results_path "$RESULTS_PATH" \
+                --inputs_json "$input_file" \
+                --update_truth "$UPDATE_TRUTH_BOOL" \
+                --commit_hash "$COMMIT_HASH" )
+            echo "Uploading the test input file: $test_input_file"
+            echo "Branch name: $branch_name"
           
             python3 scripts/firecloud_api/firecloud_api2.py \
                 upload_test_inputs \
@@ -174,27 +189,9 @@ jobs:
                 --branch_name "$branch_name" \
                 --sa-json-b64 "$SA_JSON_B64" \
                 --user "pdt-tester@warp-pipeline-dev.iam.gserviceaccount.com"
-          done
-      - name: Submit to Terra and Monitor Workflows
-        run: |
-            # Set common environment variables
-            MAX_RETRIES=2
-            RETRY_DELAY=300  # 300 seconds = 5 minutes
-            PIPELINE_NAME="TestIlluminaGenotypingArray"
-            PIPELINE_DIR="pipelines/broad/genotyping/illumina"
-            TEST_TYPE="${{ env.testType }}"
-            INPUTS_DIR="$PIPELINE_DIR/test_inputs/$TEST_TYPE"
-            USE_CALL_CACHE="${{ github.event.inputs.useCallCache || 'true' }}"
-          
-            if [ "$USE_CALL_CACHE" == "true" ]; then
-                USE_CALL_CACHE_BOOL=true
-            else
-                USE_CALL_CACHE_BOOL=false
-            fi
           
             # Create the submission_data.json file which will be the same for all inputs
             SUBMISSION_DATA_FILE="submission_data.json"
-          
             # Use a heredoc to generate the JSON file content dynamically
             cat <<EOF > "$SUBMISSION_DATA_FILE"
             {
@@ -210,55 +207,103 @@ jobs:
             }
             EOF
             echo "Created submission data file: $SUBMISSION_DATA_FILE"
-            cat "$SUBMISSION_DATA_FILE"
-            
-            # Initialize variables to aggregate statuses and outputs
-            ALL_WORKFLOW_STATUSES="Workflow ID | Status"$'\n'"--- | ---"
-            ALL_OUTPUTS=""
-            
-            # Initialize arrays to track submission and workflow statuses
-            declare -a SUBMISSION_IDS
-            declare -A WORKFLOW_STATUSES
-  
-            # Loop through each file in the appropriate test inputs directory
-            INPUTS_DIR="$PIPELINE_DIR/test_inputs/$TEST_TYPE"
-            
-            echo "Running tests with test type: $TEST_TYPE"
-          
+
             attempt=1
-          
-            for input_file in "$INPUTS_DIR"/*.json; do
-              while [ $attempt -le $MAX_RETRIES ]; do
-                echo "Attempt $attempt: Submitting job for input file: $input_file"
-                SUBMISSION_ID=$(python3 scripts/firecloud_api/firecloud_api2.py submit_job \
-                          --workspace-namespace "warp-pipelines" \
-                          --workspace-name "WARP Tests" \
-                          --sa-json-b64 "$SA_JSON_B64" \
-                          --user "pdt-tester@warp-pipeline-dev.iam.gserviceaccount.com" \
-                          --submission_data_file "$SUBMISSION_DATA_FILE")
-                echo "submission id is $SUBMISSION_ID"
-        
-                #SUBMISSION_ID=$(firecloud_action submit_job --submission_data_file "$SUBMISSION_DATA_FILE")
-            
-                if [[ "$SUBMISSION_ID" == *"404"* ]]; then
-                  echo "Error: Dockstore method not found. Retrying in $RETRY_DELAY seconds..."
-                  sleep $RETRY_DELAY
-                  ((attempt++))
-                elif [ -z "$SUBMISSION_ID" ]; then
-                  echo "Submission failed for input file: $input_file. No submission ID received."
-                  break
-                else
-                  echo "Submission successful. Submission ID: $SUBMISSION_ID"
-                  SUBMISSION_IDS+=("$SUBMISSION_ID")
-                  break
-                fi
-            
-                if [ $attempt -gt $MAX_RETRIES ]; then
-                  echo "Max retries reached. Exiting..."
-                fi
-              done
+             
+            while [ $attempt -le $MAX_RETRIES ]; do
+              echo "Attempt $attempt: Submitting job for input file: $input_file"
+              SUBMISSION_ID=$(python3 scripts/firecloud_api/firecloud_api2.py submit_job \
+                        --workspace-namespace "warp-pipelines" \
+                        --workspace-name "WARP Tests" \
+                        --sa-json-b64 "$SA_JSON_B64" \
+                        --user "pdt-tester@warp-pipeline-dev.iam.gserviceaccount.com" \
+                        --submission_data_file "$SUBMISSION_DATA_FILE")
+                
+              if [[ "$SUBMISSION_ID" == *"404"* ]]; then
+                echo "Error: Dockstore method not found. Retrying in $RETRY_DELAY seconds..."
+                sleep $RETRY_DELAY
+                ((attempt++))
+              elif [ -z "$SUBMISSION_ID" ]; then
+                echo "Submission failed for input file: $input_file. No submission ID received."
+                break
+              else
+                echo "Submission successful. Submission ID: $SUBMISSION_ID"
+                SUBMISSION_IDS+=("$SUBMISSION_ID")
+                break
+              fi
+              if [ $attempt -gt $MAX_RETRIES ]; then
+                echo "Max retries reached. Exiting..."
+              fi
             done
-          
+          done
+
+      #- name: Submit to Terra and Monitor Workflows
+      #  run: |
+      #
+      #
+      #      # Create the submission_data.json file which will be the same for all inputs
+      #      SUBMISSION_DATA_FILE="submission_data.json"
+      #
+      #      # Use a heredoc to generate the JSON file content dynamically
+      #      cat <<EOF > "$SUBMISSION_DATA_FILE"
+      #      {
+      #      "methodConfigurationNamespace": "warp-pipelines",
+      #      "methodConfigurationName": "$PIPELINE_NAME",
+      #      "useCallCache": $USE_CALL_CACHE_BOOL,
+      #      "deleteIntermediateOutputFiles": false,
+      #      "useReferenceDisks": true,
+      #      "memoryRetryMultiplier": 1.2,
+      #      "workflowFailureMode": "NoNewCalls",
+      #      "userComment": "Automated submission",
+      #      "ignoreEmptyOutputs": false
+      #      }
+      #      EOF
+      #      echo "Created submission data file: $SUBMISSION_DATA_FILE"
+      #
+      #      # Initialize variables to aggregate statuses and outputs
+      #      ALL_WORKFLOW_STATUSES="Workflow ID | Status"$'\n'"--- | ---"
+      #      ALL_OUTPUTS=""
+      #
+      #      # Initialize arrays to track submission and workflow statuses
+      #      declare -a SUBMISSION_IDS
+      #      declare -A WORKFLOW_STATUSES
+  
+      #      # Loop through each file in the appropriate test inputs directory
+      #      INPUTS_DIR="$PIPELINE_DIR/test_inputs/$TEST_TYPE"
+      #
+      #      echo "Running tests with test type: $TEST_TYPE"
+      #
+      #      attempt=1
+      #
+      #      for input_file in "$INPUTS_DIR"/*.json; do
+      #        while [ $attempt -le $MAX_RETRIES ]; do
+      #          echo "Attempt $attempt: Submitting job for input file: $input_file"
+      #          SUBMISSION_ID=$(python3 scripts/firecloud_api/firecloud_api2.py submit_job \
+      #                    --workspace-namespace "warp-pipelines" \
+      #                    --workspace-name "WARP Tests" \
+      #                    --sa-json-b64 "$SA_JSON_B64" \
+      #                    --user "pdt-tester@warp-pipeline-dev.iam.gserviceaccount.com" \
+      #                    --submission_data_file "$SUBMISSION_DATA_FILE")
+      #
+      #          if [[ "$SUBMISSION_ID" == *"404"* ]]; then
+      #            echo "Error: Dockstore method not found. Retrying in $RETRY_DELAY seconds..."
+      #            sleep $RETRY_DELAY
+      #            ((attempt++))
+      #          elif [ -z "$SUBMISSION_ID" ]; then
+      #            echo "Submission failed for input file: $input_file. No submission ID received."
+      #            break
+      #          else
+      #            echo "Submission successful. Submission ID: $SUBMISSION_ID"
+      #            SUBMISSION_IDS+=("$SUBMISSION_ID")
+      #            break
+      #          fi
+      #
+      #          if [ $attempt -gt $MAX_RETRIES ]; then
+      #            echo "Max retries reached. Exiting..."
+      #          fi
+      #        done
+      #      done
+      #