Merge branch '#139_debug' into 'master'

#139 debug

See merge request !63

src/ng6/ng6workflow.py

@@ -190,9 +190,6 @@ class NG6Workflow (BasicNG6Workflow):
         pidx = 1
         nidx = 1
         for rang, sample in enumerate(self.samples) :
-            print(sample)
-            print("sample readsi")
-            print(sample.readsi)
             if sample.name :
                 self.samples_names.append(sample.name)
             else :
@@ -686,15 +683,15 @@ class CasavaNG6Workflow(NG6Workflow):
 
             # archive the files
             #TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory()
-            saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("readsi")
+
+            saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("index")
             logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
             reads_prefixes = None
             if self.group_prefix != None :
                 # concatenate fastq
                 reads_prefixes = list((Utils.get_group_basenames(saved_files, "read")).keys())
-                logging.getLogger("CasavaNG6Workflow").debug("illumina_process reads_prefixes = " + ",".join(reads_prefixes))
                 logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
-                concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.runobj,saved_files, reads_prefixes])
+                concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.runobj,saved_files,reads_prefixes])
                 saved_files = concatenatefastq.concat_files
                 logging.getLogger("CasavaNG6Workflow").debug("illumina_process after concatenatefastq, saved_files = " + ",".join(saved_files))