diff --git a/tools/minimap2/minimap2.xml b/tools/minimap2/minimap2.xml
index 8435713747e..200ec999cd9 100644
--- a/tools/minimap2/minimap2.xml
+++ b/tools/minimap2/minimap2.xml
@@ -16,11 +16,6 @@
     <version_command>minimap2 --version</version_command>
     <command>
 <![CDATA[
-    #if $reference_source.reference_source_selector == 'history':
-        ln -f -s '$reference_source.ref_file' reference.fa &&
-    #else:
-        ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
-    #end if
     minimap2
     #if str($fastq_input.analysis_type_selector) == 'self-homology':
         -DP -k19 -w19 -m200
@@ -142,7 +137,11 @@
         -K $io_options.K
     #end if
     -t \${GALAXY_SLOTS:-4}
-    reference.fa
+    #if $reference_source.reference_source_selector == 'history':
+        '$reference_source.ref_file'
+    #else:
+        '$reference_source.ref_file.fields.path'
+    #end if
     #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
         '$fastq_input.fastq_input1'
     #else if $fastq_input.fastq_input_selector == 'paired':
@@ -151,7 +150,12 @@
          '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
     #end if
     #if str($io_options.output_format) in ('BAM', 'CRAM'):
-        -a | samtools view --no-PG -hT reference.fa
+        -a | samtools view --no-PG -hT 
+        #if $reference_source.reference_source_selector == 'history':
+            '$reference_source.ref_file'
+        #else:
+            '$reference_source.ref_file.fields.path'
+        #end if
     #end if
     #if $io_options.output_format == 'BAM':
         | samtools sort
@@ -165,7 +169,12 @@
         -@\${GALAXY_SLOTS:-2}
         -O $io_options.output_format
         $io_options.eqx
-        --reference reference.fa
+        --reference 
+        #if $reference_source.reference_source_selector == 'history':
+            '$reference_source.ref_file'
+        #else:
+            '$reference_source.ref_file.fields.path'
+        #end if
         --output-fmt-option no_ref
         -o '$alignment_output'
     #else: