Fix syntax of get_args across all scripts.

workflow/scripts/check_design.py

@@ -21,6 +21,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -98,7 +99,7 @@ def check_replicates(design):
         unique_replicates = set(replicates)
         if len(replicates) != len(unique_replicates):
             duplicated_replicates.append(experiment)
-    
+
     if len(duplicated_replicates) > 0:
         logger.error('Duplicate replicates in experiments: %s', list(duplicated_replicates))
         raise Exception("Duplicate replicates in experiments: %s" %

workflow/scripts/convert_reads.py

@@ -25,6 +25,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)

workflow/scripts/experiment_design.py

@@ -21,6 +21,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)

workflow/scripts/experiment_qc.py

@@ -25,6 +25,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)

workflow/scripts/map_qc.py

@@ -34,6 +34,7 @@ STRIP_EXTENSIONS = ['.bam', '.srt']
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)

workflow/scripts/map_reads.py

@@ -33,6 +33,7 @@ STRIP_EXTENSIONS = ['.gz', '.fq', '.fastq', '_trimmed']
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)

workflow/scripts/trim_reads.py

@@ -22,6 +22,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)

workflow/scripts/xcor.py

@@ -24,6 +24,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
+    
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)