diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
index 2fc5e975c..508aeb5fb 100755
--- a/workflows/rnaseq/main.nf
+++ b/workflows/rnaseq/main.nf
@@ -57,10 +57,6 @@ include { softwareVersionsToYAML           } from '../../subworkflows/nf-core/ut
 include { FASTQ_ALIGN_HISAT2               } from '../../subworkflows/nf-core/fastq_align_hisat2'
 include { BAM_MARKDUPLICATES_PICARD        } from '../../subworkflows/nf-core/bam_markduplicates_picard'
 include { BAM_RSEQC                        } from '../../subworkflows/nf-core/bam_rseqc'
-include { BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE as BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse'
-include { BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE as BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse'
-include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME        } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools'
-include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools'
 include { BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD } from '../../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig'
 include { BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE } from '../../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig'
 include { QUANTIFY_PSEUDO_ALIGNMENT as QUANTIFY_STAR_SALMON } from '../../subworkflows/nf-core/quantify_pseudo_alignment'