diff --git a/CholerAegon.nf b/CholerAegon.nf
index 29fa359..f2a585e 100644
--- a/CholerAegon.nf
+++ b/CholerAegon.nf
@@ -96,13 +96,15 @@ process prepare_fasta {
     input:
         tuple val(name), path(fasta)
     output:
-        tuple val(name), path("fixed_names/${name}.fasta")
+        tuple val(name), val("pre-assembled"), path("fixed_names/${name}.fasta")
     shell:
         '''
-        mkdir fixed_name
+        mkdir fixed_names
         for F in *.fa *.fasta *.fna; do
         if [ -e "$F" ]; then
-        ln -s $F fixed_names/!{name}.fasta
+        ln -s ../$F fixed_names/!{name}.fasta
+        fi
+        done
         '''
 }
 
@@ -444,13 +446,20 @@ process summary_report {
 
     input:
         path(amr_results)
-        path(fastani_results)
+        file(fastani_results)
     output:
         path("CholerAegon_summary_report_*.html")
     script:
-        """
-        summary_report.py --amr_results ${amr_results} --fastani_results ${fastani_results}
-        """
+        if (params.genome_reference) {
+            """
+            summary_report.py --amr_results ${amr_results} --fastani_results ${fastani_results}
+            """
+        }
+        else {
+            """
+            summary_report.py --amr_results ${amr_results}
+            """
+        }
 }
 
 
diff --git a/bin/summary_report.py b/bin/summary_report.py
index ce50638..df09da8 100755
--- a/bin/summary_report.py
+++ b/bin/summary_report.py
@@ -358,6 +358,8 @@ def stringify(strlst):
         self.predictiondataraw['Drug class resistances'] = data['DRUG_CLASS_RESISTANCES']
 
         def drugs_markup(str):
+            if str == '.':
+                return str
             drugs = str.split(';')
             drugs_f = []
             for d in drugs: