--- a/multiqc.xml	Wed Feb 19 16:01:14 2025 +0000
+++ b/multiqc.xml	Fri Oct 10 20:12:28 2025 +0000
@@ -212,7 +212,7 @@
 
 $flat
 $export
-
+ 
 #if $configfile == "T"
     --config '$multiqc_config'
 #end if
@@ -223,6 +223,11 @@
 ##cat ./report_data/multiqc_busco.txt &&
 cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated
 
+#if $png_plots == "true"
+    && mkdir -p ./png_plots
+    && cp ./report_plots/png/*.png ./png_plots/ | true ## don't fail if no png plots are generated
+#end if
+
     ]]></command>
     <expand macro="configfile"/>
     <inputs>
@@ -498,6 +503,7 @@
         </param>
         <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
         <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
+        <param name="png_plots" type="boolean" truevalue="true" falsevalue="false" label="Output PNG plots?" help="Choose if you want PNG plots in an output collection"/>
     </inputs>
     <outputs>
         <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage"/>
@@ -506,6 +512,10 @@
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="plots"/>
             <filter>export</filter>
         </collection>
+        <collection name="png_plot" type="list" label="${tool.name} on ${on_string}: PNG Plots">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="png_plots"/>
+            <filter>png_plots</filter>
+        </collection>
     </outputs>
     <tests>
         <expand macro="general_tests"/>
@@ -513,7 +523,7 @@
         <expand macro="bowtie2_test"/>
         <expand macro="fastqc_test"/>
         <expand macro="trimmomatic_test"/>
-        <!-- Test 10 -->
+                <!-- Test 10 -->
         <expand macro="flexbar_test"/>
         <expand macro="fastp_test"/>
         <expand macro="bismark_test"/>
@@ -544,7 +554,7 @@
         <expand macro="gtdbtk_test"/>
         <expand macro="sambamba_test"/>
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
-
+ 
     </tests>
     <help><![CDATA[
 **What it does**