Two commits. First is to use a custom factory to let us default to embl,...

Two commits. First is to use a custom factory to let us default to embl, genbank dumps and allow user override [ENSCORESW-226]. Secondly our pipeline was not RC_NAME friendly. We now inherit the default options from hive generic conf and add our own [ENSCORESW-225]

modules/Bio/EnsEMBL/Pipeline/Flatfile/DumpTypeFactory.pm

+=pod
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <dev@ensembl.org>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <helpdesk@ensembl.org>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Pipeline::Flatfile::DumpTypeFactory
+
+=head1 DESCRIPTION
+
+Small extension of the job factory to do default type submission as otherwise
+we get every type of file being produced.
+
+Allowed parameters are:
+
+=over 8
+
+=item types - The types to use; defaults to embl and genbank
+
+=back
+
+=cut
+
+package Bio::EnsEMBL::Pipeline::Flatfile::DumpTypeFactory;
+
+use strict;
+use warnings;
+
+use base qw/Bio::EnsEMBL::Hive::RunnableDB::JobFactory/;
+
+sub param_defaults {
+  my ($self) = @_;
+  return {
+    column_names => ['type'],
+    default_types => [qw/embl genbank/],
+  };
+}
+
+sub fetch_input {
+  my ($self) = @_;
+  my $user_types = $self->param('types');
+  if($user_types && @{$user_types}) {
+    $self->param('inputlist', $user_types);
+  }
+  else {
+    $self->param('inputlist', $self->param('default_types'));
+  }
+  return;
+}
+
+1;
\ No newline at end of file

modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm

@@ -24,7 +24,7 @@ sub default_options {
       
       release => software_version(),
 
-      types => [qw/embl genbank/],
+      types => [],
       
       ### Defaults 
       
@@ -67,10 +67,9 @@ sub pipeline_analyses {
       
       {
         -logic_name => 'DumpTypeFactory',
-        -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
+        -module     => 'Bio::EnsEMBL::Pipeline::Flatfile::DumpTypeFactory',
         -parameters => {
-          column_names => ['type'],
-          inputlist => $self->o('types'),
+          types => $self->o('types'),
           input_id => { species => '#species#', type => '#type#' },
           fan_branch_code => 2
         },