now the nomenclature of the new geen ids can be setup in the config.yaml file....

now the nomenclature of the new geen ids can be setup in the config.yaml file. Also 2 new rules to compile the blat results and the anchoring summary

Snakefile

@@ -13,7 +13,9 @@ rule all:
 		config['finalPrefix']+'_LC.cds.fasta',
 		config['finalPrefix']+'_LC.cds.valid.explained.txt',
 		config['finalPrefix']+'_LC.proteins.fasta',
-		config['finalPrefix']+'_gmap_differentChrom.gff3'
+		config['finalPrefix']+'_gmap_differentChrom.gff3',
+		config['finalPrefix']+'_anchoringSummary.csv',
+		config['finalPrefix']+'_blatSummary.csv'
 
 rule grepGffFeature:
 	message: " Collect selected features from GFF file"

rules/geneAnchoring.smk

@@ -130,7 +130,7 @@ rule renameGeneIds:
 		gfflc=config['finalPrefix']+'_LC.gff3',
 		correspondance=config['finalPrefix']+'_IDMapping.csv',
 		overlap=config['finalPrefix']+'_overlap.bed'
-	params: prefix='TraesCS', version='03G', source='IWGSC_v2.1'
+	params: prefix=config['gff_prefix'], version=config['gff_version'], source=config['gff_source']
 	log: config['finalPrefix']+'_IDMapping.log'
 	shell: 
 		"""
@@ -162,3 +162,21 @@ rule generateFastaSequencesLC:
 		"""
 		gffread {input.gff} -w {output.mrna} -x {output.cds} -y {output.pep} -g {input.fastaref} -W -O &> {log}
 		"""
+
+rule concatblatSummary:
+	message: " Concat all Blat summary"
+	input:blat=expand(config['results']+'/3.mapping/{chrom}/allBlat.csv', chrom=config['chromosomes'])
+	output: config['finalPrefix']+'_blatSummary.csv'
+	shell:
+		"""
+		cat {input.blat} |cut -f -3,5- 1> {output}
+		"""
+
+rule concatAnchoringSummary:
+	message: " Concat all Anchoring summary"
+	input:anchoring=expand(config['results']+'/3.mapping/{chrom}/mappingSummary.csv', chrom=config['chromosomes'])
+	output: config['finalPrefix']+'_anchoringSummary.csv'
+	shell:
+		"""
+		cat {input.anchoring} |cut -f -4,5,8- 1> {output}
+		"""