Develop (#251)

* Add note about deprecation

* Add note about deprecation

* Hot fix create-links to check for single end ss2 runs

pipeline_tools/shared/submission/create_links.py

@@ -136,7 +136,9 @@ def __init__(
             with open(analysis_protocol_list_path) as f:
                 self.analysis_protocol_list_path = json.load(f)
 
-            # If single end read then this will load an empty array
+            # If single end read then this will load a single element array with empty string
+            # This is just how bash works when piping an empty array to a file through jq
+            # array = [""]
             with open(ss2_fastq2) as f:
                 self.ss2_fastq2 = json.load(f)
 
@@ -251,7 +253,9 @@ def __ss2_intermediate_inputs__(self, index):
             }
         ]
 
-        if self.ss2_fastq2:
+        # Verify first element isn't empty string and the length is at least 1
+        # Need to at least check the case where we have a single pair
+        if not self.ss2_fastq2[0] == "" and len(self.ss2_fastq2) >= 1:
             intermediate_input.append({
                 "input_id" : self.ss2_fastq2[index],
                 "input_type" : "sequence_file"