--- a/macros.xml	Fri Oct 10 20:12:28 2025 +0000
+++ b/macros.xml	Thu Jan 15 20:39:44 2026 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.27</token>
-    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@TOOL_VERSION@">1.33</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">multiqc</xref>
@@ -11,6 +11,16 @@
             <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement>
         </requirements>
     </xml>
+    <!--This stdio rule is temporary because of an issue with CheckM2 report columns, it needs to be removed when the issue is fixed -->
+    <xml name="stdio">
+        <stdio>
+            <regex
+                match="Module 'checkm2: .*not found in the file.*"
+                source="both"
+                level="fatal"
+                description="Invalid CheckM2 TSV file: required header not found" />
+        </stdio>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/gr.244293.118</citation>
@@ -184,11 +194,11 @@
                     <has_text text="slamdunk-retained"/>
                     <has_text text="C2"/>
                     <has_n_lines n="11"/>
-                    <has_n_columns n="22"/>
+                    <has_n_columns n="24"/>
                 </assert_contents>
             </output>
             <output_collection name="plots" type="list" count="29"/>
-            <output_collection name="png_plot" type="list" count="38"/>
+            <output_collection name="png_plot" type="list" count="36"/>
         </test>
         <!--Test 02-->
         <test expect_num_outputs="2">
@@ -482,7 +492,7 @@
                     <has_text text="qualimap"/>
                     <has_text text="samblaster_duplicates"/>
                     <has_text text="quast-stats"/>
-                    <has_text text="samtools-flagstat-dp"/>
+                    <has_text text="samtools-flagstat-pct"/>
                     <has_text text="snpeff"/>
                 </assert_contents>
             </output>
@@ -507,8 +517,8 @@
                     <has_text text="snpeff_csv"/>
                     <has_text text="bamtools-mapped_reads_pct"/>
                     <has_text text="bamtools-duplicates_pct"/>
-                    <has_n_lines n="22"/>
-                    <has_n_columns n="50"/>
+                    <has_n_lines n="23"/>
+                    <has_n_columns n="55"/>
                 </assert_contents>
             </output>
         </test>
@@ -528,7 +538,7 @@
             </repeat>
             <output name="html_report" ftype="html">
                 <assert_contents>
-                    <has_size value="4766687" delta="500"/>
+                    <has_size value="2142211" delta="500"/>
                 </assert_contents>
             </output>
             <!--output name="stats" ftype="tabular">
@@ -576,7 +586,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="png_plot" type="list" count="11"/>
+            <output_collection name="png_plot" type="list" count="9"/>
             
         </test>
         <!--Test 06-->