Commit fae657c5 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

run stat_peakcalling if macs2 or seacr are set to yes

parent e8e33bf7
......@@ -733,20 +733,21 @@ if config["seacr"]["do"]:
# Peak Calling metrics
#----------------------------------
def stats_pc_input(wildcards):
if wildcards.CALLER == "macs2":
return expand(os.path.join(analysis_dir, "06-PeakCalling/{{CALLER}}/%s/{IP_REP}_peaks.{{MOD}}Peak" % (model_dir)), IP_REP=IP_ALL)
elif wildcards.CALLER == "seacr":
return expand(os.path.join(analysis_dir, "06-PeakCalling/{{CALLER}}/{IP_REP}.{{MOD}}.bed"), IP_REP=IP_ALL)
stats_peakCalling_input = stats_pc_input
stats_peakCalling_csv = os.path.join(analysis_dir, "{CALLER}_{MOD}_Peaks_metrics.out")
stats_peakCalling_marks = marks
stats_peakCalling_conds = conds
stats_peakCalling_rep = rep_flag
stats_peakCalling_log = os.path.join(analysis_dir, "06-PeakCalling/{CALLER}/{MOD}_Peaks_metrics.out")
include: os.path.join(RULES, "stats_peakCalling.rules")
final_output.extend(expand(stats_peakCalling_csv, zip, CALLER=peak_caller, MOD=mod))
if config["macs2"]["do"] or config["seacr"]["do"] :
def stats_pc_input(wildcards):
if wildcards.CALLER == "macs2":
return expand(os.path.join(analysis_dir, "06-PeakCalling/{{CALLER}}/%s/{IP_REP}_peaks.{{MOD}}Peak" % (model_dir)), IP_REP=IP_ALL)
elif wildcards.CALLER == "seacr":
return expand(os.path.join(analysis_dir, "06-PeakCalling/{{CALLER}}/{IP_REP}.{{MOD}}.bed"), IP_REP=IP_ALL)
stats_peakCalling_input = stats_pc_input
stats_peakCalling_csv = os.path.join(analysis_dir, "{CALLER}_{MOD}_Peaks_metrics_mqc.out")
stats_peakCalling_marks = marks
stats_peakCalling_conds = conds
stats_peakCalling_rep = rep_flag
stats_peakCalling_log = os.path.join(analysis_dir, "06-PeakCalling/{CALLER}/{MOD}_Peaks_metrics.out")
include: os.path.join(RULES, "stats_peakCalling.rules")
final_output.extend(expand(stats_peakCalling_csv, zip, CALLER=peak_caller, MOD=mod))
#----------------------------------
......
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