add input pointing to the mapping/chrom/temp directory containing all the...

add input pointing to the mapping/chrom/temp directory containing all the mapping files (blat, gmap)

rules/geneAnchoring.smk

@@ -11,7 +11,8 @@ rule mapHomologousRegions:
 		markersOnTarget=config['results']+"/1.filteredISBPs/{chrom}/sorted.bed"
 	output: 
 		allblat=config['results']+'/3.mapping/{chrom}/allBlat.csv',
-		summary=config['results']+'/3.mapping/{chrom}/mappingSummary.csv'
+		summary=config['results']+'/3.mapping/{chrom}/mappingSummary.csv',
+		mapping=temp(directory(config['results']+'/3.mapping/{chrom}/temp'))
 	params: dir=directory(config['results']+'/3.mapping/{chrom}')
 	log: config['results']+'/3.mapping/{chrom}/microMappingPipeline.log'
 	shell: 
@@ -24,6 +25,7 @@ rule recalcBlatMapped:
 	input: 
 		allBlat=config['results']+'/3.mapping/{chrom}/allBlat.csv',
 		summary=config['results']+'/3.mapping/{chrom}/mappingSummary.csv',
+		mapping=config['results']+'/3.mapping/{chrom}/temp',
 		refQuery=config['queryFasta'],
 		faiQuery=config['queryFasta']+'.fai',
 		refTarget=config['targetFasta'],
@@ -37,17 +39,20 @@ rule recalcBlatMapped:
 		"""
 rule gtCleanBlatGff:
 	message: " Clean the gff file recalculated based on Blat fine mapping for chromosome {wildcards.chrom}"
-	input: config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget.gff3'
+	input: gff=config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget.gff3',
+		mapping=config['results']+'/3.mapping/{chrom}/temp'
 	output: temp(config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget-clean.gff3')
 	log: config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget-clean.log'
 	shell: 
 		"""
-		gt gff3 -fixregionboundaries -sort -tidy -retainids {input} 1> {output} 2> {log}
+		gt gff3 -fixregionboundaries -sort -tidy -retainids {input.gff} 1> {output} 2> {log}
 		"""
 
 rule gmapRescue:
 	message: " Rescue anchoring of failed genes with gmap for chrom {wildcards.chrom}"
-	input: blat=config['results']+'/3.mapping/{chrom}/allBlat.csv', wholeGenomeFasta=config['targetFasta']
+	input: blat=config['results']+'/3.mapping/{chrom}/allBlat.csv', 
+		wholeGenomeFasta=config['targetFasta'],
+		mapping=config['results']+'/3.mapping/{chrom}/temp'
 	output: txt=config['results']+'/4.gmapRescue/{chrom}.txt',
 		targetgff=temp(config['results']+'/4.gmapRescue/{chrom}.target.gff3'),
 		wholegenomegff=temp(config['results']+'/4.gmapRescue/{chrom}.wholeGenome.gff3')
@@ -61,6 +66,7 @@ rule gmapRescue:
 rule recalcGmapRescue:
 	message: "Recalc the coordinates of the GMAP on target GFF3 files for chromosome {wildcards.chrom}"
 	input: gff=config['results']+'/4.gmapRescue/{chrom}.target.gff3',
+		mapping=config['results']+'/3.mapping/{chrom}/temp'
 	output: temp(config['results']+'/4.recalcGmap/{chrom}/recalc.gff3')
 	params: anchoringDir=config['results']+'/3.mapping/{chrom}',
 		bindir=os.getcwd()
@@ -73,7 +79,8 @@ rule recalcGmapRescue:
 rule saveGmapWG:
 	message: "Save the GMAP results of genes mapped on Whole Genome"
 	input: gff=config['results']+'/4.gmapRescue/{chrom}.wholeGenome.gff3',
-		map=config['chromMapID']
+		map=config['chromMapID'],
+		mapping=config['results']+'/3.mapping/{chrom}/temp'
 	output: gff=temp(config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome.gff3'),
 		gfferror=temp(config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome_differentChrom.gff3')
 	log: config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome.log'
@@ -88,7 +95,8 @@ rule mergeFinalGff3:
 	message: " Merge Final GFF3 files: blat.gff3, rescue.gff3 and wholeGenome.gff3"
 	input: blat=config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget-clean.gff3',
 		rescue=config['results']+'/4.recalcGmap/{chrom}/recalc.gff3', 
-		wg=config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome.gff3'
+		wg=config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome.gff3',
+		mapping=config['results']+'/3.mapping/{chrom}/temp'
 	output: annot=temp(config['results']+'/5.FINAL/{chrom}/annotation.gff3')
 	log: annot=config['results']+'/5.FINAL/{chrom}/annotation.log'
 	shell: