update python3 required changes to filter iterators to list and dict …

…keys to list

pypiper/ngstk.py

@@ -312,7 +312,7 @@ class of inputs (which can in turn be a string or a list).
         if any(isinstance(i, list) for i in input_args):
             # We have a list of lists. Process each individually.
             local_input_files = list()
-            n_input_files = len(filter(bool, input_args))
+            n_input_files = len(list(filter(bool, input_args)))
             print("Number of input file sets: " + str(n_input_files))
 
             for input_i, input_arg in enumerate(input_args):
@@ -549,8 +549,8 @@ def temp_func(
             if type(output_files) != list:
                 output_files = [output_files]
 
-            n_input_files = len(filter(bool, input_files))
-            n_output_files = len(filter(bool, output_files))
+            n_input_files = len(list(filter(bool, input_files)))
+            n_output_files = len(list(filter(bool, output_files)))
 
             total_reads = sum(
                 [

pypiper/utils.py

@@ -864,14 +864,14 @@ def _determine_args(argument_groups, arguments, use_all_args=False):
     # Define the argument groups.
     args_by_group = {
         "pypiper": ["recover", "new-start", "dirty", "force-follow", "testmode"]
-        + LOGGING_CLI_OPTDATA.keys(),
+        + [*LOGGING_CLI_OPTDATA],
         "config": ["config"],
         "checkpoint": ["stop-before", "stop-after"],
         "resource": ["mem", "cores"],
         "looper": ["config", "output-parent", "mem", "cores", "pipeline-name"],
         "common": ["input", "sample-name"],
         "ngs": ["sample-name", "input", "input2", "genome", "single-or-paired"],
-        "logmuse": LOGGING_CLI_OPTDATA.keys(),
+        "logmuse": [*LOGGING_CLI_OPTDATA],
         "pipestat": [
             "pipestat-namespace",
             "pipestat-record-id",