Fix bug while running DE with batch

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