bug in mapHomologousRegions shell command: need to use {wildcards.chrom}...

bug in  mapHomologousRegions shell command: need to use {wildcards.chrom} instead of {chrom} in the shell to properly expand the chrom variable

rules/geneAnchoring.smk

@@ -2,27 +2,28 @@ rule mapHomologousRegions:
 	message: " mapping homologous regions of both references using ISBPs markers as anchors"
 	input: 
 		#closestMarkers=config['results']+'/2.mergedClosestMarkers.txt',
-		marker5prime=config['results']+'/2.closestbedUpstream.txt',
-		marker3prime=config['results']+'/2.downstreamClosest.txt',
+		marker5prime=config['results']+'/2.closestbed_split/{chrom}.upstream.txt',
+		marker3prime=config['results']+'/2.closestbed_split/{chrom}.downstream.txt',
 		refQuery=config['queryFasta'],
 		faiQuery=config['queryFasta']+'.fai',
 		refTarget=config['targetFasta'],
 		faiTarget=config['targetFasta']+'.fai',
-		markersOnTarget=config['results']+"/1.filteredISBPs.sorted.bed"
-	output: directory(config['results']+'/3.mapping')
-	log: config['results']+'/3.mapping.log'
+		markersOnTarget=config['results']+"/1.filteredISBPs.sorted.{chrom}.bed"
+	output: dir=directory(config['results']+'/3.mapping/{chrom}')
+	log: config['results']+'/3.mapping/{chrom}/microMappingPipeline.log'
 	shell: 
 		"""
-		echo bin/microMappingPipeline.py {input.marker5prime} {input.marker3prime} {output} {input.refQuery} {input.refTarget} {input.markersOnTarget} &> {log}
+		echo bin/microMappingPipeline.py {input.marker5prime} {input.marker3prime} {output.dir} {input.refQuery} {input.refTarget} {input.markersOnTarget} &> {log}
+		echo fgrep -h 'Could not identify a pair of marker to use to anchor' {log} |cut -d ' ' -f 15|cut -d '.' -f 1|sort > config['results']+'/3.mapping/{wildcards.chrom}/noMarkerPairs.txt'
 		"""
 
 rule gmapRescue:
 	message: " Rescue anchoring of failed genes with gmap"
-	input: anchoringDir=directory(config['results']+'/3.mapping'),
-		blastdb=config['blastdb']
-	output: config['results']+'/4.gmapRescue.txt'
-	log: config['results']+'/4.gmapRescue.log'
+	input: anchoringDir=config['results']+'/3.mapping/{chrom}'
+	output: config['results']+'/4.gmapRescue/{chrom}.txt'
+	params: blastdb=config['blastdb']
+	log: config['results']+'/4.gmapRescue/{chrom}.log'
 	shell:
 		"""
-		bin/gmapRescue.sh {input.anchoringDir} {input.blastdb} 1> {output} 2> {log}
+		echo bin/gmapRescue.sh {input.anchoringDir} {params.blastdb} 1> {output} 2> {log}
 		"""