new parameters to setup the nomenclature of the new gene IDs

config.yaml

 ##### QUERY related files/parameters (refseqv1.0)
 # GFF annotatin to transfert
-annotationQuery: 'data/IWGSC_v1.2_20200508.gff3'
+annotationQuery: 'data/IWGSC_v1.2_20200615.gff3'
 # feature type used for anchoring on target genome
 featureType: 'gene'
 # FASTA of the query (used to check the sequences after the coordinates are calculated on the target genome)
 queryFasta: 'data/161010_Chinese_Spring_v1.0_pseudomolecules.fasta'
 # blastdb of all mrnas. used to rescue genes which have failed in the transfert using the targeted approache
-blastdb: 'data/IWGSC_v1.2_20200508.transcripts.fasta'
+blastdb: 'data/IWGSC_v1.2_20200615.transcripts.fasta'
 # map of all chromosome ids --> NEED TO BE UPDATED in another version WITH ONE ARRAY FOR THE QUERY AND ONE ARRAY FOR THE TARGET GENOME ASSEMBLY
 chromosomes: ['1A', '2A', '3A', '4A', '5A', '6A', '7A', '1B', '2B', '3B', '4B', '5B', '6B', '7B', '1D', '2D', '3D', '4D', '5D', '6D', '7D', 'U']
 refChrom: ['chr1A', 'chr1B', 'chr1D', 'chr2A', 'chr2B', 'chr2D', 'chr3A', 'chr3B', 'chr3D', 'chr4A', 'chr4B', 'chr4D', 'chr5A', 'chr5B', 'chr5D', 'chr6A', 'chr6B', 'chr6D', 'chr7A', 'chr7B', 'chr7D', 'chrUn']
@@ -25,8 +25,14 @@ mapq: 30
 mismatches: 0
 
 ##### OUTPUT directory
-results: 'results'
-finalPrefix: 'IWGSC_refseqv2.1_annotv2.0'
+results: 'results_200615'
+finalPrefix: 'IWGSC_refseqv2.1_annotv2.0_200617'
 # this file contains two columns: the first is the chromosome name as it appears in the genome.fasta of the new reference,
 # and the second the chromosome name as it will appear in the new gene Names
 chromMapID: 'data/chromosomeMappingID.csv'
+
+##### Nomenclature for final gene IDs
+# used in rule renameGeneIds (rules/geneAnchoring.smk)
+gff_prefix: 'TraesCS'
+gff_version: '03G'
+gff_source: 'IWGSC_v2.1'
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