add temp file definition

rules/preprocessISBP.smk

 rule filterBam:
 	message: "Filtering BAM file of ISBPs"
 	input: config['isbpBam']
-	output: temp(config['results']+'/1.filteredISBPs.bam')
+	output: config['results']+'/1.filteredISBPs.bam'
 	params: mapq=config['mapq'], mismatches=config['mismatches']
 	log: config['results']+'/1.filterBam.log'
 	shell: "bin/filterBam.py {input} {output} {params.mapq} {params.mismatches} &> {log}"
@@ -28,7 +28,7 @@ rule dumpISBPsID:
 
 rule splitISBP:
 	message: "Split isbps per chromosome"
-	input: config['results']+"/1.filteredISBPs.sorted.bed"
+	input: config['results']+"/1.filteredISBPs/sorted.bed"
 	output: temp(config['results']+"/1.filteredISBPs/{chrom}/sorted.bed")
 	log: config['results']+"/1.filteredISBPs/{chrom}/sorted.log"
 	params: 'Chr{chrom}'