try updating usercomment

broadinstitute · Jan 10, 2025 · a9b93ac · a9b93ac
1 parent 72d40bc
commit a9b93ac
Showing 1 changed file with 16 additions and 32 deletions.
diff --git a/.github/workflows/test_illumina_genotyping_array.yml b/.github/workflows/test_illumina_genotyping_array.yml
@@ -222,24 +222,24 @@ jobs:
           RESULTS_PATH="gs://broad-gotc-test-storage/$DOCKSTORE_PIPELINE_NAME/results/$CURRENT_TIME"
           
           # Create the submission_data.json file which will be the same for all inputs
-          #SUBMISSION_DATA_FILE="submission_data.json"
+          SUBMISSION_DATA_FILE="submission_data.json"
                     
-          ## Use a heredoc to generate the JSON file content dynamically
-          #cat <<EOF > "$SUBMISSION_DATA_FILE"
-          #{
-          #  "methodConfigurationNamespace": "$WORKSPACE_NAMESPACE",
-          #  "methodConfigurationName": "$METHOD_CONFIG_NAME",
-          #  "useCallCache": $USE_CALL_CACHE_BOOL,
-          #  "deleteIntermediateOutputFiles": false,
-          #  "useReferenceDisks": true,
-          #  "memoryRetryMultiplier": 1.2,
-          #  "workflowFailureMode": "NoNewCalls",
-          #  "userComment": "Automated submission",
-          #  "ignoreEmptyOutputs": false
-          #}
-          #EOF
+          # Use a heredoc to generate the JSON file content dynamically
+          cat <<EOF > "$SUBMISSION_DATA_FILE"
+          {
+            "methodConfigurationNamespace": "$WORKSPACE_NAMESPACE",
+            "methodConfigurationName": "$METHOD_CONFIG_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" 
+          echo "Created submission data file: $SUBMISSION_DATA_FILE" 
           
           # 1. Submit all jobs first and store their submission IDs
           for input_file in "$INPUTS_DIR"/*.json; do
@@ -250,22 +250,6 @@ jobs:
                 --branch_name "$BRANCH_NAME" )
             echo "Uploading the test input file: $test_input_file"
           
-            SUBMISSION_DATA_FILE="submission_data.json"
-          
-            cat <<EOF > "$SUBMISSION_DATA_FILE"
-            {
-              "methodConfigurationNamespace": "$WORKSPACE_NAMESPACE",
-              "methodConfigurationName": "$METHOD_CONFIG_NAME",
-              "useCallCache": $USE_CALL_CACHE_BOOL,
-              "deleteIntermediateOutputFiles": false,
-              "useReferenceDisks": true,
-              "memoryRetryMultiplier": 1.2,
-              "workflowFailureMode": "NoNewCalls",
-              "userComment": "$test_input_file",
-              "ignoreEmptyOutputs": false
-            }
-            EOF
-          
             python3 scripts/firecloud_api/firecloud_api.py \
                 upload_test_inputs \
                 --workspace-namespace $WORKSPACE_NAMESPACE \