Adjusting nested map task

FredHutch · Dec 21, 2024 · 08f70c2 · 08f70c2
1 parent 7e789cf
commit 08f70c2
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/mapTypeTest/mapTypeTest.wdl b/mapTypeTest/mapTypeTest.wdl
@@ -93,9 +93,13 @@ task process_nested_map {
         String patient_id
         Map[String, String] patient_data
         Array[String] samples_for_patient
-        String sample_type = patient_data[samples_for_patient[0]]
     }
 
+    # First get the first sample ID
+    String first_sample = samples_for_patient[0]
+    # Then use it to index the patient data
+    String sample_type = patient_data[first_sample]
+
     command {
         echo "Processing patient ${patient_id} with sample type ${sample_type}"
         for sample in ${sep=' ' samples_for_patient}; do