diff --git a/snakePipes/shared/rules/multiQC.snakefile b/snakePipes/shared/rules/multiQC.snakefile
index 1ec4b8db1..13f6933e7 100755
--- a/snakePipes/shared/rules/multiQC.snakefile
+++ b/snakePipes/shared/rules/multiQC.snakefile
@@ -78,14 +78,14 @@ def multiqc_input_check(return_value):
             infiles.append( expand(aligner+"/{sample}.markdup.bam", sample = samples) +
                     expand("Sambamba/{sample}.markdup.txt", sample = samples) +
                     expand("deepTools_qc/estimateReadFiltering/{sample}_filtering_estimation.txt",sample=samples))
-            infiles.append( expand("allelic_bams/{sample}.{suffix}.sorted.bam", sample = samples,suffix = allele_suffix) )
+            infiles.append( expand("allelic_bams/{sample}.{suffix}.sorted.bam", sample = samples,suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']) )
             indir += aligner
             indir += " Sambamba "
             indir += " deepTools_qc "
             indir += " allelic_bams "
         if "allelic-whatshap" in mode and fromBAM:
-            infiles.append( expand("filtered_bam/{sample}.filtered.bam.txt", sample = samples) )
-            infiles.append( expand("allelic_bams/{sample}.{suffix}.sorted.bam", sample = samples,suffix = allele_suffix) )
+            infiles.append( expand("filtered_bam/{sample}.filtered.bam", sample = samples) )
+            infiles.append( expand("allelic_bams/{sample}.{suffix}.sorted.bam", sample = samples,suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']) )
             infiles.append( expand("featureCounts/{sample}.allelic_counts.txt", sample = samples) )
             indir += " filtered_bam " + " featureCounts "
             indir += " allelic_bams "