Update run_param_config.py

added new genome Nakaseomyces glabratus to run_param_config
mskcc · Sep 24, 2024 · b4ab63c · b4ab63c
1 parent 22297a7
commit b4ab63c
Showing 1 changed file with 15 additions and 0 deletions.
diff --git a/scripts/run_param_config.py b/scripts/run_param_config.py
@@ -131,6 +131,7 @@ def get_ordered_dic(unordered_dic):
 		"E.Lambda": "elambda",
 		"Plasmid": "ecolik12",
 		"Pig": "sscrofa11",
+		"N. glabratus": "cbs138",
 		# FOR NEW ENTRIES
 		# "{regex}": "{GENOME}"
 
@@ -324,6 +325,20 @@ def get_ordered_dic(unordered_dic):
 						GTAG: "grcz11"
 				}
 		},
+		"cbs138": {
+				DEFAULT: {
+						GENOME: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa",
+						REFERENCE: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa"
+				},
+				"RNA": {
+						GENOME: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa",
+						REFERENCE: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.fa",
+						REF_FLAT: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.CLEAN.gtf.refflat",
+						RIBOSOMAL_INTERVALS: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.CLEAN.gtf.rRNA.intervals",
+						GTF: "/igo/work/nabors/genomes/N.glabratus/GCF/GCF_010111755_1_ASM1011175v1_genomic.CLEAN.gtf",
+						GTAG: "cbs138"
+				}
+		},
 		"ce10": {
 				DEFAULT: {
 						GENOME: "/igo/work/genomes/C.elegans/ce10/BWA_0.7.5a/ce10.fa",