diff --git a/Snakefile_atac.smk b/Snakefile_atac.smk
index 18b72ffc9ddbbcd3bf099a7b5d6a11699c5220d3..89098321f00a7d2b3f5291967f316c972272fe04 100755
--- a/Snakefile_atac.smk
+++ b/Snakefile_atac.smk
@@ -867,8 +867,8 @@ if len(conds) > 1 and config["differential_analysis"]["do"]:
     chipflowr_init_input = feature_counts_output_count
     chipflowr_init_conds = conds
     chipflowr_init_rep = rep_noidr
-    chipflowr_init_method = method
-    chipflowr_init_norm = norm
+    chipflowr_init_method = config["differential_analysis"]["method"]
+    chipflowr_init_norm = config["differential_analysis"]["normalisation"]
     if config["differential_analysis"]["spikes"] and config["design"]["spike"]:
         chipflowr_init_spikes = spikes_counting_output_json
         chipflowr_init_input_done = spikes_counting_output_json