--- a/multiqc.xml	Tue Feb 11 10:13:08 2025 +0000
+++ b/multiqc.xml	Tue Feb 18 23:18:25 2025 +0000
@@ -23,6 +23,19 @@
         <import>star_plugin.xml</import>
         <import>trimmomatic_plugin.xml</import>
         <import>vcftools_plugin.xml</import>
+        <import>kraken_plugin.xml</import>
+        <import>diamond_plugin.xml</import>
+        <import>bakta_plugin.xml</import>
+        <import>freyja_plugin.xml</import>
+        <import>checkm_plugin.xml</import>
+        <import>pairtools_plugin.xml</import>
+        <import>porechop_plugin.xml</import>
+        <import>snippy_plugin.xml</import>
+        <import>metaphlan_plugin.xml</import>
+        <import>bbduk_plugin.xml</import>
+        <import>megahit_plugin.xml</import>
+        <import>nonpareil_plugin.xml</import>
+        <import>gtdbtk_plugin.xml</import>
         <import>sambamba_plugin.xml</import>
     </macros>
     <expand macro="bio_tools"/>
@@ -144,6 +157,32 @@
         @TRIMMOMATIC_COMMAND@
     #elif str($repeat.software_cond.software) == "vcftools"
         @VCFTOOLS_COMMAND@
+    #elif str($repeat.software_cond.software) == "kraken"
+        @KRAKEN_COMMAND@
+    #elif str($repeat.software_cond.software) == "diamond"
+        @DIAMOND_COMMAND@
+    #elif str($repeat.software_cond.software) == "bakta"
+        @BAKTA_COMMAND@
+    #elif str($repeat.software_cond.software) == "freyja"
+        @FREYJA_COMMAND@
+    #elif str($repeat.software_cond.software) == "checkm"
+        @CHECKM_COMMAND@
+    #elif str($repeat.software_cond.software) == "pairtools"
+        @PAIRTOOLS_COMMAND@
+    #elif str($repeat.software_cond.software) == "porechop"
+        @PORECHOP_COMMAND@
+    #elif str($repeat.software_cond.software) == "snippy"
+        @SNIPPY_COMMAND@
+    #elif str($repeat.software_cond.software) == "metaphlan"
+        @METAPHLAN_COMMAND@
+    #elif str($repeat.software_cond.software) == "bbduk"
+        @BBDUK_COMMAND@
+    #elif str($repeat.software_cond.software) == "megahit"
+        @MEGAHIT_COMMAND@
+    #elif str($repeat.software_cond.software) == "nonpareil"
+        @NONPAREIL_COMMAND@
+    #elif str($repeat.software_cond.software) == "gtdbtk"
+        @GTDBTK_COMMAND@
     #elif str($repeat.software_cond.software) == "sambamba"
         @SAMBAMBA_COMMAND@
     #else if str($repeat.software_cond.software) == "custom_content":
@@ -253,6 +292,19 @@
                     <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option>
                     <option value="trimmomatic">Trimmomatic</option>
                     <option value="vcftools">VCFTools</option>
+                    <option value="kraken">Kraken 1 or 2</option>
+                    <option value="diamond">DIAMOND</option>
+                    <option value="bakta">Bakta</option>
+                    <option value="freyja">Freyja</option>
+                    <option value="checkm">CheckM</option>
+                    <option value="pairtools">pairtools</option>
+                    <option value="porechop">Porechop</option>
+                    <option value="snippy">Snippy</option>
+                    <option value="metaphlan">MetaPhlAn</option>
+                    <option value="bbduk">BBDuk</option>
+                    <option value="megahit">MEGAHIT</option>
+                    <option value="nonpareil">Nonpareil</option>
+                    <option value="gtdbtk">GTDB-Tk</option>
                     <!--<option value="verifybamid">VerifyBAMID</option>-->
                     <!--Custom-->
                     <option value="custom_content">Custom Content</option>
@@ -353,6 +405,45 @@
                 <when value="vcftools">
                     <expand macro="vcftools_form"/>
                 </when>
+                <when value="kraken">
+                    <expand macro="kraken_form"/>
+                </when>
+                <when value="diamond">
+                    <expand macro="diamond_form"/>
+                </when>
+                <when value="bakta">
+                    <expand macro="bakta_form"/>
+                </when>
+                <when value="freyja">
+                    <expand macro="freyja_form"/>
+                </when>
+                <when value="checkm">
+                    <expand macro="checkm_form"/>
+                </when>
+                <when value="pairtools">
+                    <expand macro="pairtools_form"/>
+                </when>
+                <when value="porechop">
+                    <expand macro="porechop_form"/>
+                </when>
+                <when value="snippy">
+                    <expand macro="snippy_form"/>
+                </when>
+                <when value="metaphlan">
+                    <expand macro="metaphlan_form"/>
+                </when>
+                <when value="bbduk">
+                    <expand macro="bbduk_form"/>
+                </when>
+                <when value="megahit">
+                    <expand macro="megahit_form"/>
+                </when>
+                <when value="nonpareil">
+                    <expand macro="nonpareil_form"/>
+                </when>
+                <when value="gtdbtk">
+                    <expand macro="gtdbtk_form"/>
+                </when>
                 <when value="sambamba">
                     <expand macro="sambamba_form"/>
                 </when>
@@ -432,6 +523,19 @@
         <expand macro="gatk_test"/>
         <expand macro="bamtools_test"/>
         <expand macro="pycoqc_test"/>
+        <expand macro="kraken_test"/>
+        <expand macro="diamond_test"/>
+        <expand macro="bakta_test"/>
+        <expand macro="freyja_test"/>
+        <expand macro="checkm_test"/>
+        <expand macro="pairtools_test"/>
+        <expand macro="porechop_test"/>
+        <expand macro="snippy_test"/>
+        <expand macro="metaphlan_test"/>
+        <expand macro="bbduk_test"/>
+        <expand macro="megahit_test"/>
+        <expand macro="nonpareil_test"/>
+        <expand macro="gtdbtk_test"/>
         <expand macro="sambamba_test"/>
 
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->