--- a/multiqc.xml	Fri Oct 10 20:11:35 2025 +0000
+++ b/multiqc.xml	Thu Jan 15 20:38:43 2026 +0000
@@ -21,6 +21,7 @@
         <import>salmon_plugin.xml</import>
         <import>samtools_plugin.xml</import>
         <import>star_plugin.xml</import>
+        <import>sylphtax_plugin.xml</import>
         <import>trimmomatic_plugin.xml</import>
         <import>vcftools_plugin.xml</import>
         <import>kraken_plugin.xml</import>
@@ -28,6 +29,7 @@
         <import>bakta_plugin.xml</import>
         <import>freyja_plugin.xml</import>
         <import>checkm_plugin.xml</import>
+        <import>checkm2_plugin.xml</import>
         <import>pairtools_plugin.xml</import>
         <import>porechop_plugin.xml</import>
         <import>snippy_plugin.xml</import>
@@ -41,6 +43,7 @@
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <version_command>multiqc --version</version_command>
     <command detect_errors="aggressive">
 <![CDATA[
@@ -148,6 +151,8 @@
         @LN_FILES@
     #else if str($repeat.software_cond.software) == "star":
         @STAR_COMMAND@
+    #elif str($repeat.software_cond.software) == "sylphtax"
+        @SYLPHTAX_COMMAND@
     #elif str($repeat.software_cond.software) == "tophat"
         #for $file in $repeat.software_cond.input
             @ESCAPE_IDENTIFIER@
@@ -168,6 +173,8 @@
         @FREYJA_COMMAND@
     #elif str($repeat.software_cond.software) == "checkm"
         @CHECKM_COMMAND@
+    #elif str($repeat.software_cond.software) == "checkm2"
+        @CHECKM2_COMMAND@
     #elif str($repeat.software_cond.software) == "pairtools"
         @PAIRTOOLS_COMMAND@
     #elif str($repeat.software_cond.software) == "porechop"
@@ -297,6 +304,7 @@
                     <option value="snpeff">SnpEff</option>
                     <option value="sortmerna">SortMeRNA</option>
                     <option value="star">STAR</option>
+                    <option value="sylphtax">Sylph-tax</option>
                     <!--<option value="supernova">Supernova</option>-->
                     <!--<option value="theta2">THeTA2</option>-->
                     <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option>
@@ -307,6 +315,7 @@
                     <option value="bakta">Bakta</option>
                     <option value="freyja">Freyja</option>
                     <option value="checkm">CheckM</option>
+                    <option value="checkm2">CheckM2</option>
                     <option value="pairtools">pairtools</option>
                     <option value="porechop">Porechop</option>
                     <option value="snippy">Snippy</option>
@@ -406,6 +415,9 @@
                 <when value="star">
                     <expand macro="star_form"/>
                 </when>
+                <when value="sylphtax">
+                    <expand macro="sylphtax_form"/>
+                </when>
                 <when value="tophat">
                     <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/>
                 </when>
@@ -430,6 +442,9 @@
                 <when value="checkm">
                     <expand macro="checkm_form"/>
                 </when>
+                <when value="checkm2">
+                    <expand macro="checkm2_form"/>
+                </when>
                 <when value="pairtools">
                     <expand macro="pairtools_form"/>
                 </when>
@@ -553,6 +568,8 @@
         <expand macro="nonpareil_test"/>
         <expand macro="gtdbtk_test"/>
         <expand macro="sambamba_test"/>
+        <expand macro="checkm2_test"/>
+        <expand macro="sylphtax_test"/>
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
  
     </tests>