Dedup bam as input to QC rules - remove pool for Seacr and from IA input

Snakefile

@@ -511,7 +511,7 @@ if config["bamCoverage"]["do"]:
 #----------------------------------
 # Estimate Library Complexity
 #----------------------------------
-lib_complexity_input = os.path.join(analysis_dir, "02-Mapping/{SAMPLE}_{REF}_sort.bam")
+lib_complexity_input = "{}/{{SAMPLE}}_{{REF}}_sort_dedup{}.bam".format(biasedRegions_dir, biasedRegions)
 lib_complexity_metrics = os.path.join(analysis_dir, "05-QC/Complexity/{SAMPLE}_{REF}_metrics.txt")
 lib_complexity_log_std = os.path.join(analysis_dir, "05-QC/Complexity/logs/{SAMPLE}_{REF}_complexity.out")
 lib_complexity_log_err = os.path.join(analysis_dir, "05-QC/Complexity/logs/{SAMPLE}_{REF}_complexity.err")
@@ -522,7 +522,7 @@ include: os.path.join(RULES, "EstimateLibraryComplexity.rules")
 # plot Fingerprint
 #----------------------------------
 def IPandINPUT(wildcards):
-    return [os.path.join(analysis_dir,"02-Mapping/{{IP}}_{}_sort.bam".format(ref)), str(os.path.join(analysis_dir,"02-Mapping/") + IP_INPUT[IP_INPUT.IP == wildcards.IP].iloc[0]['INPUT'] + "_{}_sort.bam".format(ref))]
+    return [os.path.join(analysis_dir,"{}/{{IP}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)), str(os.path.join(analysis_dir, biasedRegions_dir +"/") + IP_INPUT[IP_INPUT.IP == wildcards.IP].iloc[0]['INPUT'] + "_{}_sort_dedup{}.bam".format(ref, biasedRegions))]
 
 
 plotFingerprint_input = IPandINPUT
@@ -693,7 +693,7 @@ if config["seacr"]["do"]:
     seacr_output = os.path.join(analysis_dir, "06-PeakCalling/seacr/{{SAMPLE}}.{}.bed".format(config["seacr"]["threshold"]))
     seacr_logs_std = os.path.join(analysis_dir, "06-PeakCalling/seacr/logs/{SAMPLE}_seacr_calling.out")
     seacr_logs_err = os.path.join(analysis_dir, "06-PeakCalling/seacr/logs/{SAMPLE}_seacr_calling.err")
-    final_output.extend(expand(seacr_output, SAMPLE=(IP_ALL+ IP_PPR + PPR_POOL)))
+    final_output.extend(expand(seacr_output, SAMPLE=IP_ALL))
     include: os.path.join(RULES, "seacr.rules")   
 
 
@@ -763,16 +763,8 @@ def IA_input(wildcards):
     elif wildcards.CALLER == "seacr":
         return expand(os.path.join(analysis_dir, "06-PeakCalling/{{CALLER}}/{{IP_IDR}}_{CASE}.{{MOD}}.bed"), CASE=rep)
 
-def IA_pool(wildcards):
-    if wildcards.CALLER == "macs2":
-        return os.path.join(analysis_dir, "06-PeakCalling/{{CALLER}}/{}/{{IP_IDR}}_PPRPool_peaks.{{MOD}}Peak".format(model_dir))
-    elif wildcards.CALLER == "seacr":
-        return os.path.join(analysis_dir, "06-PeakCalling/{CALLER}/{IP_IDR}_PPRPool.{MOD}.bed")
-
-
 if model in ["broad"] or config["compute_idr"]["intersectionApproach"] or config["seacr"]["do"] :
     intersectionApproach_input_rep = IA_input
-    intersectionApproach_input_pool = IA_pool
     intersectionApproach_logs = os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/logs/{IP_IDR}_IA_{MOD}peaks.o")
     intersectionApproach_output = os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{IP_IDR}_IA.{MOD}Peak")
     if model in ["broad"] :