diff --git a/modules/Bio/EnsEMBL/Analysis/Hive/Config/StarScallopRnaseq.pm b/modules/Bio/EnsEMBL/Analysis/Hive/Config/StarScallopRnaseq.pm
index ca07ef763..5c2da2972 100644
--- a/modules/Bio/EnsEMBL/Analysis/Hive/Config/StarScallopRnaseq.pm
+++ b/modules/Bio/EnsEMBL/Analysis/Hive/Config/StarScallopRnaseq.pm
@@ -436,6 +436,8 @@ sub pipeline_analyses {
       -parameters => {
         output_dir => $self->o('input_dir'),
         download_method => $self->o('download_method'),
+        read_length_table => $self->o('read_length_table'),
+
         uncompress => 0,
       },
       -flow_into => {
diff --git a/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/HiveDownloadData.pm b/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/HiveDownloadData.pm
index 02db4fa66..58393da46 100644
--- a/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/HiveDownloadData.pm
+++ b/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/HiveDownloadData.pm
@@ -99,6 +99,35 @@ sub param_defaults {
 sub fetch_input {
   my ($self) = @_;
 
+  # Early exit if file already present and verified
+  my $filepath = catfile($self->param_required('output_dir'), basename($self->param_required('url')));
+  if (-e $filepath && $self->param_is_defined('md5sum')) {
+    my $digest = Digest::MD5->new();
+    open(my $fh, $filepath) || $self->throw("Could not open '$filepath': $!");
+    binmode $fh;
+    my $md5sum = $digest->addfile($fh)->hexdigest;
+    close($fh) || $self->throw("Could not close '$filepath': $!");
+    if ($md5sum eq $self->param('md5sum')) {
+      $self->say_with_header("File '$filepath' already exists and md5sum matches, skipping download", 1);
+      my $final_file = $self->param('uncompress') ? ($filepath =~ /^(\S+)\.\w+$/)[0] : $filepath;
+
+      my $already_processed = 0;
+      eval {
+        my $sth = $self->db->dbc->prepare('SELECT read_length FROM '.$self->param('read_length_table').' WHERE fastq = ?');
+        $sth->execute(basename($final_file));
+        my $row = $sth->fetchrow_arrayref;
+        $already_processed = 1 if $row;
+        $sth->finish;
+      };
+
+      unless ($already_processed) {
+        $self->dataflow_output_id({filename => $final_file}, $self->param('_branch_to_flow_to'));
+      }
+      $self->input_job->autoflow(0);
+      $self->complete_early("File already present and verified");
+    }
+  }
+
   if ($] =~ '^5.024') {
     $self->throw("Perl 5.24 doesn't work with this module. If you manage to make it work, please submit a pull-request");
   }
@@ -249,9 +278,30 @@ sub pre_cleanup {
   my ($self) = @_;
 
   my $filepath = catfile($self->param_required('output_dir'), basename($self->param_required('url')));
+
   if (-e $filepath) {
-    unlink $filepath;
+    if ($self->param_is_defined('md5sum')) {
+      my $digest = Digest::MD5->new();
+      open(my $fh, $filepath) || $self->throw("Could not open '$filepath': $!");
+      binmode $fh;
+      my $md5sum = $digest->addfile($fh)->hexdigest;
+      close($fh) || $self->throw("Could not close '$filepath': $!");
+
+      unless ($md5sum eq $self->param('md5sum')) {
+        $self->say_with_header("File '$filepath' exists but md5sum mismatch (expected: ".$self->param('md5sum').", got: $md5sum), removing for re-download");
+        unlink $filepath or $self->warning("Could not remove '$filepath': $!");
+      }
+      # if md5 matches: do nothing here, fetch_input handles the early exit
+    }
+    else {
+      $self->say_with_header("File '$filepath' already exists but no md5sum defined, removing it to force a clean download");
+      unlink $filepath or $self->warning("Could not remove '$filepath': $!");
+    }
+  }
+  else {
+    $self->say_with_header("File '$filepath' does not exist, nothing to clean up");
   }
 }
 
 1;
+