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