few more clean ups

Author: jerowe

lib/BioX/Workflow/Command/run/Utils/Files/ResolveDeps.pm

@@ -131,11 +131,14 @@ sub print_stats_rules {
     $self->fh->say( $self->comment_char );
     $self->fh->say("");
 
+    foreach my $sample ($self->all_samples){
+    $self->fh->say("");
     $self->fh->say(
-        "biox stats --samples " . join( ',', @{ $self->samples } ) . " \\" );
+        "biox stats --samples " . $sample . " \\" );
     $self->fh->say( "--select_rules " . $rule . " \\" );
     $self->fh->say( "-w " . $self->cached_workflow );
     $self->fh->say("");
+    }
 }
 
 =head3 dedeps

lib/BioX/Workflow/Command/stats.pm

@@ -148,7 +148,7 @@ sub gen_row {
 
         my $rel = '';
         $rel = File::Spec->abs2rel($file) if $self->use_full;
-        $rel = basename($file);
+        $rel = basename($file) unless $self->use_full;
 
         #Add the filename
         push( @trow, $rel );
@@ -168,7 +168,6 @@ sub gen_row {
         }
         $self->table_log->addRow( \@trow );
     }
-
 }
 
 sub iter_file_samples {
@@ -192,7 +191,6 @@ sub iter_file_samples {
         }
         $self->gen_row( $file, $cond, $sample, \@sample_files );
     }
-
 }
 
 sub iter_file_chunks {