diff --git a/Snakefile_atac.smk b/Snakefile_atac.smk index b12a57261700a197f26ceade9ddfd61378a4ae74..2a47c07be432c045ccd79a037525a3390e5745bb 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 #----------------------------------