From 230e36fdfd19b35fa6802230cb77e0b42c575504 Mon Sep 17 00:00:00 2001
From: Amina Alioua <aalioua@pasteur.fr>
Date: Wed, 14 Aug 2024 16:49:18 +0200
Subject: [PATCH] Update code: -clean Snakefile
---
Snakefile_atac.smk | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/Snakefile_atac.smk b/Snakefile_atac.smk
index b12a572..2a47c07 100755
--- a/Snakefile_atac.smk
+++ b/Snakefile_atac.smk
@@ -764,7 +764,7 @@ if len(all_peak_caller.keys()) >= 1:
merge_peakcaller_logerr = os.path.join(analysis_dir,"13-MergePeaks/logs/{SAMPLE}_mergePeaks_{FORM}.err")
merge_peakcaller_all = os.path.join(analysis_dir,"13-MergePeaks/concat/{SAMPLE}_all_{FORM}.bed")
- # To recheck for the columns !
+ # To recheck for the columns ?
merge_peakcaller_options = "-c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max"
# Default mode for now (genrich and lanceotron by default)
mod = 'narrow'
@@ -772,8 +772,6 @@ if len(all_peak_caller.keys()) >= 1:
include: os.path.join(RULES, "merge_peakcaller.rules")
final_output.extend(expand(merge_peakcaller_output,SAMPLE=ALL_IP_PC,FORM=mod))
-FORMAT = [all_peak_caller[peak_caller][1] for peak_caller in all_peak_caller.keys()]
-
#----------------------------------
# Run differential analysis
#----------------------------------
--
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