Update run_param_config.py

adding the genone reference fasta file for Candida_parapsilosis to the script
mskcc · Nov 23, 2024 · 0a1e8dd · 0a1e8dd
1 parent 287da08
commit 0a1e8dd
Showing 1 changed file with 15 additions and 0 deletions.
diff --git a/scripts/run_param_config.py b/scripts/run_param_config.py
@@ -133,6 +133,7 @@ def get_ordered_dic(unordered_dic):
 		"Plasmid": "ecolik12",
 		"Pig": "sscrofa11",
 		"N. glabratus": "cbs138",
+		"C. parapsilosis": "cdc317",
 		# FOR NEW ENTRIES
 		# "{regex}": "{GENOME}"
 
@@ -340,6 +341,20 @@ def get_ordered_dic(unordered_dic):
 						GTAG: "cbs138"
 				}
 		},
+		"cdc317": {
+				DEFAULT: {
+						GENOME: "/igo/work/nabors/genomes/Candida_parapsilosis/GCF_000182765.1_ASM18276v2_CDC317.fa",
+						REFERENCE: "/igo/work/nabors/genomes/Candida_parapsilosis/GCF_000182765.1_ASM18276v2_CDC317.fa"
+				},
+				"RNA": {
+						GENOME: "/igo/work/nabors/genomes/Candida_parapsilosis/GCF_000182765.1_ASM18276v2_CDC317.fa",
+						REFERENCE: "/igo/work/nabors/genomes/Candida_parapsilosis/GCF_000182765.1_ASM18276v2_CDC317.fa",
+						REF_FLAT: "",
+						RIBOSOMAL_INTERVALS: "",
+						GTF: "/igo/work/nabors/genomes/Candida_parapsilosis/GTF/GCF_000182765.1_ASM18276v2_CDC317.gtf",
+						GTAG: "cdc317"
+				}
+		},
 		"ce10": {
 				DEFAULT: {
 						GENOME: "/igo/work/genomes/C.elegans/ce10/BWA_0.7.5a/ce10.fa",