--- a/macros.xml	Fri Jul 30 06:29:50 2021 +0000
+++ b/macros.xml	Thu Nov 30 17:57:59 2023 +0000
@@ -1,5 +1,8 @@
 <macros>
-    <token name="@VERSION@">0.13.2</token>
+    <token name="@VERSION@">0.14.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.01</token>
+
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@VERSION@">nanopolish</requirement>
@@ -19,6 +22,52 @@
             <output name="output_index_readdb" file="reads.fasta.index.readdb" />
  -->
 
+
+    <token name="@PREPROCESS_INPUTS@"><![CDATA[
+        ln -s '$input_merged' reads.fasta && 
+ 
+        mkdir fast5_files &&
+        #if $input_reads_raw.extension == 'fast5':
+             ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar':
+            ln -s '$input_reads_raw' fast5_files.tar &&
+            tar -xf fast5_files.tar -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
+            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
+            tar -xjf fast5_files.tar.bz2 -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.xz':
+            ln -s '$input_reads_raw' fast5_files.tar.xz &&
+            tar -xf fast5_files.tar.xz -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.gz':
+            ln -s '$input_reads_raw' fast5_files.tar.gz &&
+            tar -xzf fast5_files.tar.gz -C fast5_files &&
+
+        #else:
+            echo 'Unsupported fast5 input type' &&
+            exit 1 &&
+
+        #end if
+
+        nanopolish index 
+        -d fast5_files/
+        #if $adv.input_seq_summary:
+          -s '$adv.input_seq_summary'
+        #end if 
+        reads.fasta &&
+
+        ln -s '$b' reads.bam &&
+        ln -s '${b.metadata.bam_index}' reads.bam.bai &&
+        #if $reference_source.reference_source_selector == 'history':
+            ln -f -s '$reference_source.ref_file' genome.fa &&
+        #else:
+            ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
+        #end if
+    ]]></token>
+
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/nmeth.3444</citation>