From bebc9e859ee537262c74dc14742ef5ef705ddc79 Mon Sep 17 00:00:00 2001
From: Rachel LEGENDRE <rachel.legendre@pasteur.fr>
Date: Thu, 6 Feb 2025 17:00:49 +0100
Subject: [PATCH] Fix bug while running DE with batch
---
Snakefile_atac.smk | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile_atac.smk b/Snakefile_atac.smk
index 18b72ff..8909832 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
--
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