diff --git a/modules/convert_input_from_minknow.nf b/modules/convert_input_from_minknow.nf
index 4506c48e37ce2f8c13f9aa184f1efca3a623f210..a906269f485b58eb9a719eb7e7824a4d76c585fd 100755
--- a/modules/convert_input_from_minknow.nf
+++ b/modules/convert_input_from_minknow.nf
@@ -1,4 +1,4 @@
-process CONVERT_INPUT_FROM_MINKNOW {
+process CONVERT_INPUT_FROM_MINKNOW_BARCODED {
 
     publishDir "results/${params.out_dir}/minknow_converted_input", mode: "copy", overwrite: true
 
@@ -46,3 +46,49 @@ process CONVERT_INPUT_FROM_MINKNOW {
         """
 }
 
+
+process CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED {
+
+    publishDir "results/${params.out_dir}/minknow_converted_input", mode: "copy", overwrite: true
+
+    label 'cpu'
+
+    input:
+        path input
+    output:
+        path "*.bam", emit: bam
+        path "*.txt", emit: txt
+
+    script:
+        """
+        # Define the input directory path
+        input_dir="${input.toString()}"
+
+        # Check if the input directory exists
+        if [ -d "\${input_dir}" ]; then
+            echo "Input directory exists."
+        else
+            echo "Input directory does not exist."
+            exit 1
+        fi
+
+        # Find all 'pass' directories, follow symlinks with -L
+	find -L "\${input_dir}" -type d \\( -name 'pass' -o -name '*pass*' \\) -print0 | while IFS= read -r -d '' pass_dir; do 
+	    
+	    ## Get the name of the input directory for file naming 
+	    parent_dir="\${pass_dir%/*}"; parent_dir="\${parent_dir##*/}"
+ 
+                # Check if the pass directory contains any BAM files
+	        bam_files=(\$(find -L "\$pass_dir" -type f -name '*.bam' | grep -v 'iltered'))	
+		if [ \${#bam_files[@]} -gt 0 ]; then
+                    # Merge BAM files using samtools
+                    output_bam="./\${parent_dir}.bam"
+                    samtools merge "./\$output_bam" "\${bam_files[@]}"
+
+                    # Generate summary with dorado
+                    dorado summary "\$output_bam" > "./\${parent_dir}.txt"
+                fi
+        done
+        """
+}
+
diff --git a/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf b/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
index f4656eefb3c302fc396dcd368d5de882763da730..e68e76caad4a43e1f405d10bf427d09415951228 100755
--- a/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
+++ b/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
@@ -3,7 +3,7 @@
 include {PYCOQC_NO_FILTER ; PYCOQC_FILTER} from '../modules/pycoqc.nf'
 include {FILTER_BAM} from '../modules/filter_bam.nf'
 include {MAKE_QC_REPORT} from '../modules/num_reads_report.nf'
-include {CONVERT_INPUT_FROM_MINKNOW} from '../modules/convert_input_from_minknow.nf' 
+include {CONVERT_INPUT_FROM_MINKNOW_BARCODED; CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED} from '../modules/convert_input_from_minknow.nf' 
 
 workflow FILTERING_AND_QC_FROM_MINKNOW {
         
@@ -13,11 +13,17 @@ workflow FILTERING_AND_QC_FROM_MINKNOW {
         quality_score
 
     main:
-	 
-    CONVERT_INPUT_FROM_MINKNOW(input)
-
-    FILTER_BAM(CONVERT_INPUT_FROM_MINKNOW.out.bam.flatten().map {file -> tuple(file.baseName, file) }.toSortedList( { a, b -> a[0] <=> b[0] } ).flatten().buffer(size:2),
-	CONVERT_INPUT_FROM_MINKNOW.out.txt.toSortedList( { a, b -> a.baseName <=> b.baseName } ).flatten(), mapq)
+    
+    if (params.is_barcoded == true) {
+    	CONVERT_INPUT_FROM_MINKNOW_BARCODED(input)
+	converted_input = CONVERT_INPUT_FROM_MINKNOW_BARCODED.out
+    } else if (params.is_barcoded == false) {
+	CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED(input)
+	converted_input = CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED.out
+    }
+
+    FILTER_BAM(converted_input.bam.flatten().map {file -> tuple(file.baseName, file) }.toSortedList( { a, b -> a[0] <=> b[0] } ).flatten().buffer(size:2),
+	converted_input.txt.toSortedList( { a, b -> a.baseName <=> b.baseName } ).flatten(), mapq)
 
     PYCOQC_NO_FILTER(FILTER_BAM.out.id, FILTER_BAM.out.total_bam, FILTER_BAM.out.total_bai, FILTER_BAM.out.filtered_bam, 
     FILTER_BAM.out.filtered_bai, FILTER_BAM.out.unfiltered_flagstat, FILTER_BAM.out.filtered_flagstat, FILTER_BAM.out.txt,  quality_score)
diff --git a/workflow/main.nf b/workflow/main.nf
index f85e809f0056c3c363a07877e1872c934a6a37e1..be8790855739d55c90f436599b90097ad922fa34 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -36,6 +36,8 @@ Basecall quality score threshold for basecalling (make sure it is the same as in
 MAPQ filtering threshold							                        : ${params.mapq}
 
 Minimum number of mapped reads per sample/barcode for a file to be included in analysis			: ${params.min_mapped_reads_thresh}
+
+Are input bam files barcoded? (Only relevant to "step_2_from_minknow" option)				: ${params.is_barcoded}
 ======================================================================================================================================================================================
  
 """
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 363ab57001c5ccf1e8c7d82b56f3ae5636412a12..b410106f4afb8792e9a61e416e2fd2b77729fc9c 100755
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -56,6 +56,11 @@ params.steps_2_and_3_input_directory = "None"
 // MultiQC config
 params.multiqc_config = "None"
 
+// Are the files from MinKNOW barcoded or not 
+params.is_barcoded = true
+
+
+
 
 if (params.step == 1) {