--- a/sniffles.xml	Wed Sep 25 13:25:22 2024 +0000
+++ b/sniffles.xml	Thu Sep 26 11:44:04 2024 +0000
@@ -16,6 +16,13 @@
         <![CDATA[
 ln -f -s '${input}' input.bam &&
 ln -f -s '${input.metadata.bam_index}' input.bam.bai &&
+#if $reference_genome.genome_type_select != "None":
+    #if $reference_genome.genome_type_select == "indexed":
+        ln -f -s '${reference_genome.genome.fields.path}' 'reference.fa' &&
+    #else:
+        ln -f -s '${reference_genome.genome}' 'reference.fa' &&
+    #end if
+#end if
 sniffles
 -t \${GALAXY_SLOTS:-2}
 -i 'input.bam'
@@ -23,11 +30,7 @@
 ## must set allow-overwrite since the new output vcf file exists
 --allow-overwrite
 #if $reference_genome.genome_type_select != "None":
-    #if $reference_genome.genome_type_select == "indexed":
-        --reference '${reference_genome.genome.fields.path}' 
-    #else:
-        --reference '${reference_genome.genome}' 
-    #end if
+   --reference 'reference.fa' 
 #end if
 ## general_options
     --minsupport '$general_options.minsupport'
@@ -109,6 +112,15 @@
             <param name="mosaic" value="--mosaic"/>
             <output name="output" file="expected_outcome5.vcf" lines_diff="4"/>
         </test>
+       <test> <!-- test 6 - reference -->
+            <param name="input" value="reads_region.bam"/>
+            <conditional name="reference_genome">
+                <param name="genome_type_select" value="history"/>
+                <param name="genome" value="humsamp.fa"/>
+                <param name="genome.ext" value="fasta"/>
+            </conditional>
+            <output name="output" file="expected_outcome6.vcf" lines_diff="4"/>
+        </test>
     </tests>
     <help>
         <![CDATA[