Update to main config to run long read module by default

modules/Bio/EnsEMBL/Analysis/Hive/Config/Genome_annotation_conf.pm

@@ -87,7 +87,7 @@ sub default_options {
     'skip_projection'           => '0', # Will skip projection process if 1
     'skip_lastz'                => '0', # Will skip lastz if 1 (if skip_projection is enabled this is irrelevant)
     'skip_rnaseq'               => '0', # Will skip rnaseq analyses if 1
-    'skip_long_read'            => '1', # Will skip long read analyses if 1
+    'skip_long_read'            => '0', # Will skip long read analyses if 1
     'skip_ncrna'                => '0', # Will skip ncrna process if 1
     'skip_cleaning'             => '0', # Will skip the cleaning phase, will keep more genes/transcripts but some lower quality models may be kept
     'mapping_required'          => '0', # If set to 1 this will run stable_id mapping sometime in the future. At the moment it does nothing
@@ -6704,7 +6704,7 @@ sub pipeline_analyses {
         -logic_name => 'fan_long_read',
         -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
         -parameters => {
-                         cmd => 'if [ "#skip_long_read#" -ne "0" ]; then exit 42; else exit 0;fi',
+                         cmd => 'if [ "#skip_long_read#" -eq "0" ] && [ -e "'.$self->o('long_read_summary_file').'" ] || [ -e "'.$self->o('long_read_summary_file_genus').'" ]; then exit 0; else exit 42;fi',
                          return_codes_2_branches => {'42' => 2},
 	},
         -flow_into  => {