Correct error in Bwa.IndexWrapper

Conf.txt

@@ -79,28 +79,23 @@ fasta : ./demo/references/AAV-RSV-GFP.fa.gz
 
 #   List of output required for the reference separated by any blank space. See above
 #   for valid values (list of strings)
-output : bam	sam	bedgraph	bed	covgraph	variant
+output : bam	sam	bedgraph	bed	covgraph
 
 [Ref2]
 name : Backbone
 fasta : ./demo/references/Bacterial_backbone.fa.gz
-output : bam	sam	bedgraph	bed	covgraph	variant
+output : bam	sam	bedgraph	bed	covgraph
 
 [Ref3]
 name : Helper 
 fasta : ./demo/references/Helper_plasmid.fa.gz
-output : bam	sam	bedgraph	bed	covgraph	variant
+output : bam	sam	bedgraph	bed	covgraph
 
 [Ref4]
 name : Ad5
 fasta : ./demo/references/Ad5_in_293_genome.fa.gz
 output : bam	bedgraph
 
-[Ref5]
-name : human_genome
-fasta : ./demo/references/HG_GRCh38_chr22.fa.gz
-output : bam	bedgraph	
-
 #####################
 #    FASTQ FILES    #
 #####################

pyDNA/Bwa/IndexWrapper.py

@@ -49,6 +49,12 @@ class NewIndex(object):
             if isinstance(ref, str):
                 self.ref = ref
                 self._make_index()
+
+            # If list at one element = same thing
+            elif isinstance(ref, list) and len(ref) == 1:
+                self.ref = ref[0]
+                self._make_index()
+
             # If severel references, merged them, make index and remove the merged reference file
             elif isinstance(ref, list):
                 print("Merge references files for indexation")
@@ -76,7 +82,7 @@ class NewIndex(object):
         # Run the command line without stdin and asking both stdout and stderr
         start_time = time()
         stderr = run_command(cmd, stdin=None, ret_stderr=True, ret_stdout=False)
-        
+
         print (stderr)
         print ("Index created in {}s\n".format(round(time()-start_time, 3)))