diff --git a/seqnado/workflow/snakefile_consensus_peaks b/seqnado/workflow/snakefile_consensus_peaks
deleted file mode 100644
index 61f752e0..00000000
--- a/seqnado/workflow/snakefile_consensus_peaks
+++ /dev/null
@@ -1,42 +0,0 @@
-import os
-import sys
-import shutil
-from datetime import datetime
-import glob
-from snakemake.utils import min_version
-import seqnado.utils
-import pandas as pd
-import pathlib
-
-ASSAY = "CONSENUS_PEAKS"
-configfile: "config_consensus_peaks.yml"
-container: "library://asmith151/seqnado/seqnado_pipeline:latest"
-
-
-seqnado.utils.format_config_dict(config)
-
-
-# Get experiment design
-# Require a fn column and a group column
-design_path = pathlib.Path(config["design"])
-if design_path.exists():
-    DESIGN = pd.read_csv(design_path, sep="[\s+,\t]", engine="python")
-    assert DESIGN.shape[0] > 0, "No samples found in design file"
-
-else:
-    raise ValueError("No design file found")
-
-
-SAMPLE_NAMES = [pathlib.Path(fn).stem for fn in DESIGN.fn]
-GROUPS = DESIGN.group.unique().tolist()
-
-
-include: "rules/alignment_post_processing.smk"
-include: "rules/peak_call.smk"
-include: "rules/pileup.smk"
-include: "rules/consensus_peaks.smk"
-
-
-rule all:
-    input:
-        peaks=expand("seqnado_output/consensus_peaks/{group}.bed", group=GROUPS),
diff --git a/seqnado/workflow/snakefile_rna b/seqnado/workflow/snakefile_rna
index 6cafa0c3..e81f5f6a 100644
--- a/seqnado/workflow/snakefile_rna
+++ b/seqnado/workflow/snakefile_rna
@@ -59,7 +59,7 @@ include: "rules/heatmap.smk"
 
 # Define output files
 ANALYSIS_OUTPUT = utils.define_output_files(
-    sample_names=SAMPLE_NAMES, assay=ASSAY, can_run_deseq2=CAN_RUN_DESEQ2, project_name=PROJECT_NAME,  **config
+    snakemake_design=DESIGN, sample_names=SAMPLE_NAMES, assay=ASSAY, can_run_deseq2=CAN_RUN_DESEQ2, project_name=PROJECT_NAME,  **config
 )
 
 rule all:
diff --git a/seqnado/workflow/snakefile_snp b/seqnado/workflow/snakefile_snp
index 16a26bfd..220ff7be 100755
--- a/seqnado/workflow/snakefile_snp
+++ b/seqnado/workflow/snakefile_snp
@@ -41,7 +41,8 @@ include: "rules/hub.smk"
 include: "rules/qc.smk"
 include: "rules/variant.smk"
 
-ANALYSIS_OUTPUT = utils.define_output_files(sample_names=SAMPLE_NAMES,
+ANALYSIS_OUTPUT = utils.define_output_files(snakemake_design=DESIGN,
+                                            sample_names=SAMPLE_NAMES,
                                             assay=ASSAY,
                                             **config)
 
@@ -69,4 +70,4 @@ onerror:
     shutil.copyfile(log, log_out)
     print(
         f"An error occurred. Please check the log file {log_out} for more information."
-    )
\ No newline at end of file
+    )