added method Bio::EnsEMBL::Pipeline::RunnableDB::branch_code

so that branch_code is set explicitly rather than replying on the return
value of the write_output method.  Switched Worker.pm to use this value.

modules/Bio/EnsEMBL/Hive/Extensions.pm

@@ -169,5 +169,13 @@ sub Bio::EnsEMBL::Pipeline::RunnableDB::global_cleanup
   return 1;
 }
 
+sub Bio::EnsEMBL::Pipeline::RunnableDB::branch_code
+{
+  my $self = shift;
+  $self->{'_branch_code'} = shift if(@_);
+  $self->{'_branch_code'}=1 unless($self->{'_batch_size'});
+  return $self->{'_branch_code'};
+}
+
 1;
 

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -357,12 +357,12 @@ sub run_module_with_job
   $runObj->run;
 
   $job->status('WRITE_OUTPUT');
-  my $branch_code = $runObj->write_output;
+  $runObj->write_output;
 
   #runnableDB is allowed to alter its input_id on output
   #This modified input_id is passed as input to the next jobs in the graph
   $job->input_id($runObj->input_id);
-  $job->branch_code($branch_code);
+  $job->branch_code($runObj->branch_code);
 
   return 1;
 }