show query/cmd/filename when debug is on

modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm

@@ -205,6 +205,9 @@ sub _get_rows_from_list {
 sub _get_rows_from_query {
     my ($self, $inputquery) = @_;
 
+    if($self->debug()) {
+        warn qq{inputquery = "$inputquery"\n};
+    }
     my @rows = ();
     my $sth = $self->dbh()->prepare($inputquery);
     $sth->execute();
@@ -228,6 +231,9 @@ sub _get_rows_from_query {
 sub _get_rows_from_open {
     my ($self, $input_file_or_pipe, $delimiter, $parse_header) = @_;
 
+    if($self->debug()) {
+        warn qq{input_file_or_pipe = "$input_file_or_pipe"\n};
+    }
     my @rows = ();
     open(FILE, $input_file_or_pipe) or die "Could not open '$input_file_or_pipe' because: $!";
     while(my $line = <FILE>) {

modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm

@@ -108,6 +108,10 @@ sub run {
             # Perform parameter substitution:
         my $sql = $self->param_substitute($unsubst_sql);
 
+         if($self->debug()) {
+             warn qq{sql = "$sql"\n};
+         }
+
         $dbh->do( $sql ) or die "Could not run '$sql': ".$dbh->errstr;
 
         my $insert_id_name  = '_insert_id_'.$counter++;

modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm

@@ -108,6 +108,10 @@ sub run {
  
     my $cmd = $self->param('cmd');
 
+    if($self->debug()) {
+        warn qq{cmd = "$cmd"\n};
+    }
+
     $self->dbc and $self->dbc->disconnect_when_inactive(1);    # release this connection for the duration of system() call
 
     if(my $return_value = system($cmd)) {