Index: trunk/ippScripts/scripts/phase3.pl
===================================================================
--- trunk/ippScripts/scripts/phase3.pl	(revision 11319)
+++ trunk/ippScripts/scripts/phase3.pl	(revision 11333)
@@ -113,5 +113,7 @@
 }
 
-unless (defined $workdir) {
+if (defined $workdir) {
+    $workdir = $ipprc->convert_filename_absolute( $workdir );
+} else {
     my $example = ${$files}[0]->{b1_uri}; # Example filename
     my ($vol, $dir, $file) = File::Spec->splitpath( $example );
@@ -122,5 +124,4 @@
 my $outputRoot = $exp_tag . '.p3'; # Root output name
 $outputRoot = File::Spec->catfile( $workdir, $outputRoot );
-$outputRoot = $ipprc->convert_filename_absolute($outputRoot);
 my $list1Name = $outputRoot . '.b1.list'; # Name for the input file list for binning 1
 my $list2Name = $outputRoot . '.b2.list'; # Name for the input file list for binning 2