diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm
index 7d92c09b7244493255b8067b8639f8efe2c00559..36f4a48aab4baffd444c7c1621e43e4c9fd43976 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/FlatfileChecker_conf.pm
@@ -43,19 +43,17 @@ sub pipeline_analyses {
       -parameters => {
         inputcmd => 'find '.$self->o('base_path').q{ -type f -name '*.dat.gz'},
         column_names => ['file'],
-        randomize => 1,
-        input_id_template => '{ file => "#file#" }'
+        randomize => 1
       },
       -input_ids  => [ {} ],
       -flow_into  => {
-        # 1 => 'Notify',
-        2 => ['CheckFlatfile'],
+        2 =>  { CheckFlatfile => { file => '#file#'} }
       },
     },
     {
       -logic_name => 'CheckFlatfile',
       -module     => 'Bio::EnsEMBL::Pipeline::Flatfile::CheckFlatfile',
-      -hive_capacity => 15,
+      -analysis_capacity => 15,
       -rc_name => 'dump',
     },
   ];
diff --git a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm
index 3c6bc61515610de8698b7f44256e0be4499c5c88..000a93161143ae5aaf0e0f6973d709387717cbdd 100644
--- a/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/PipeConfig/Flatfile_conf.pm
@@ -70,17 +70,19 @@ sub pipeline_analyses {
         -module     => 'Bio::EnsEMBL::Pipeline::Flatfile::DumpTypeFactory',
         -parameters => {
           types => $self->o('types'),
-          input_id_template => '{ species => "#species#", type => "#type#" }',
-          fan_branch_code => 2
         },
-        -flow_into  => { 2 => ['DumpFlatfile', 'ChecksumGenerator'] },
+        -flow_into  => {
+          2 => { 'DumpFlatfile' => { species => "#species#", type => "#type#" },
+                 'ChecksumGenerator' => { species => "#species#", type => "#type#" },
+          },
+        },
       },
       
       {
         -logic_name => 'DumpFlatfile',
         -module     => 'Bio::EnsEMBL::Pipeline::Flatfile::DumpFile',
         -max_retry_count  => 1,
-        -hive_capacity    => 10,
+        -analysis_capacity => 10,
         -rc_name => 'dump',
       },
       
@@ -90,7 +92,7 @@ sub pipeline_analyses {
         -logic_name => 'ChecksumGenerator',
         -module     => 'Bio::EnsEMBL::Pipeline::Flatfile::ChecksumGenerator',
         -wait_for   => [qw/DumpFlatfile/],
-        -hive_capacity => 10, 
+        -analysis_capacity => 10, 
       },
       
       ####### NOTIFICATION