diff --git a/seqnado/workflow/rules/qc.smk b/seqnado/workflow/rules/qc.smk
index 8424693c..6358bedc 100644
--- a/seqnado/workflow/rules/qc.smk
+++ b/seqnado/workflow/rules/qc.smk
@@ -93,19 +93,44 @@ use rule samtools_stats as samtools_stats_filtered with:
     output:
         stats="seqnado_output/qc/alignment_filtered/{sample}.txt",
 
-
-rule multiqc:
-    input:
-        expand(
+def get_fastqc_files(wildcards):
+    
+    
+    single_end_assays = [name for name in SAMPLE_NAMES if DESIGN.query(name).is_paired == True]
+    paired_end_assays = [name for name in SAMPLE_NAMES if DESIGN.query(name).is_paired == False]   
+    
+    fastqc_raw_paired = expand(
             "seqnado_output/qc/fastqc_raw/{sample}_{read}_fastqc.html",
-            sample=SAMPLE_NAMES,
+            sample=paired_end_assays,
             read=[1, 2],
         ),
-        expand(
+    fastqc_trimmed_paired = expand(
             "seqnado_output/qc/fastqc_trimmed/{sample}_{read}_fastqc.html",
-            sample=SAMPLE_NAMES,
+            sample=paired_end_assays,
             read=[1, 2],
         ),
+    
+    fastqc_raw_single = expand(
+            "seqnado_output/qc/fastqc_raw/{sample}_fastqc.html",
+            sample=single_end_assays,
+        ),
+    
+    fastqc_trimmed_single = expand(
+            "seqnado_output/qc/fastqc_trimmed/{sample}_fastqc.html",
+            sample=single_end_assays,
+        ),
+    
+    all_qc_files = []
+    for files in [fastqc_raw_paired, fastqc_trimmed_paired, fastqc_raw_single, fastqc_trimmed_single]:
+        if files:
+            all_qc_files.extend(files)
+    
+    return all_qc_files
+
+
+rule multiqc:
+    input:
+        get_fastqc_files,
         expand("seqnado_output/qc/alignment_raw/{sample}.txt", sample=SAMPLE_NAMES),
         expand(
             "seqnado_output/qc/alignment_filtered/{sample}.txt",