--- a/panta.xml	Tue Sep 16 11:28:02 2025 +0000
+++ b/panta.xml	Mon Oct 13 07:59:25 2025 +0000
@@ -13,12 +13,12 @@
 
         #if $input_type.input_type_selector == "gff":
             #for gff in $input_type.input_gff
-                #set identifier = re.sub('[^\s\w\-\\.]','_',str($gff.element_identifier))
-                ln -fs '$gff' '$input_directory/$identifier' &&
+                #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
+                cp '$gff' '$input_directory/$filename' &&
             #end for
         #elif $input_type.input_type_selector == "tsv":
-            #set identifier = re.sub('[^\s\w\-\\.]','_',str($input_type.input_tsv.element_identifier))
-            ln -fs '$input_type.input_tsv' '$input_directory/$identifier' &&
+            #set $filename = '%s.tsv' % re.sub('[^\w_-]', '_', str($input_type.input_tsv.element_identifier))
+            cp '$input_type.input_tsv' '$input_directory/$filename' &&
         #end if
 
         #if $mode.select_mode == "main":
@@ -402,7 +402,7 @@
             </output>
             <output name="core_gene_alignment" ftype="txt">
                 <assert_contents>
-                    <has_n_lines n="96690" delta='3'/>
+                    <has_n_lines n="96130" delta='3'/>
                 </assert_contents>
             </output>
             <output name="pan_genome_reference" ftype="txt">
@@ -709,4 +709,4 @@
         <citation type="doi">10.6084/m9.figshare.23724705</citation>
     </citations>
     <expand macro="creator"/>
-</tool>
\ No newline at end of file
+</tool>