Merge branch 'issue#221' into 'master'

Modification of BWA algo #221

See merge request !134

workflows/components/contaminationsearch.py

@@ -74,9 +74,8 @@ class ContaminationSearch (Analysis):
         for current_databank in self.databanks:
             databank_basename = os.path.basename(current_databank).split(".")[0]
             unmerged_name_files = self.get_outputs('{basename_woext}_names.' + databank_basename + '.txt', self.sequence_files)
-            self.add_shell_execution(self.get_exec_path("bwa") + ' aln ' + current_databank + ' $1 2>> $3 | ' + 
-                                     self.get_exec_path("bwa") + ' samse ' + current_databank + ' - $1 2>> $3 | ' + self.get_exec_path("samtools") + 
-                                    ' view -SF 260 - 2>> $3 | cut -f1 - 2>> $3 | sort - > $2 2>> $3', 
+            self.add_shell_execution(self.get_exec_path("bwa") + ' mem ' + current_databank + ' $1 2>> $3 | ' +
+                                     self.get_exec_path("samtools") + ' view -SF 260 - 2>> $3 | cut -f1 - 2>> $3 | sort - > $2 2>> $3', 
                                      cmd_format='{EXE} {IN} {OUT}', map=True,
                                      inputs=self.sequence_files, outputs=[unmerged_name_files, self.conta_stderr[databank_basename]])