Supporting empty array specification and using the value specified in the param_defaults

modules/Bio/EnsEMBL/Pipeline/FASTA/Base.pm

@@ -5,11 +5,28 @@ use warnings;
 use base qw/Bio::EnsEMBL::Hive::Process/;
 
 use Bio::EnsEMBL::Utils::Exception qw/throw/;
+use Bio::EnsEMBL::Utils::Scalar qw/check_ref/;
 use File::Find;
 use File::Spec;
 use File::Path qw/mkpath/;
 use POSIX qw/strftime/;
 
+# Takes in a key, checks if the current $self->param() was an empty array
+# and replaces it with the value from $self->param_defaults()
+sub reset_empty_array_param {
+  my ($self, $key) = @_;
+  my $param_defaults = $self->param_defaults();
+  my $current = $self->param($key); 
+  my $replacement = $self->param_defaults()->{$key};
+  if(check_ref($current, 'ARRAY') && check_ref($replacement, 'ARRAY')) {
+    if(! @{$current}) {
+      $self->fine('Restting param %s because the given array was empty', $key);
+      $self->param($key, $replacement);
+    }
+  }
+  return;
+}
+
 sub get_Slices {
   my ($self, $type) = @_;
   my $sa = $self->get_DBAdaptor($type)->get_SliceAdaptor();

modules/Bio/EnsEMBL/Pipeline/FASTA/SpeciesFactory.pm

@@ -70,7 +70,6 @@ use warnings;
 use base qw/Bio::EnsEMBL::Pipeline::FASTA::Base/;
 
 use Bio::EnsEMBL::Registry;
-use Bio::EnsEMBL::Utils::Scalar qw/wrap_array/;
 
 sub param_defaults {
   my ($self) = @_;
@@ -84,6 +83,9 @@ sub param_defaults {
 sub fetch_input {
   my ($self) = @_;
   
+  $self->reset_empty_array_param('sequence_type_list');
+  $self->reset_empty_array_param('db_types');
+  
   my $core_dbas = $self->get_DBAdaptors();
   $self->info('Found %d core DBAdaptor(s) to process', scalar(@{$core_dbas}));
   $self->param('dbas', $core_dbas);