update dragen reference file location

mskcc · Feb 3, 2025 · 39039e8 · 39039e8
1 parent e8741f9
commit 39039e8
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/dragen_GLP.py b/scripts/dragen_GLP.py
@@ -10,7 +10,7 @@
 
 
 OUTPUT_PATH = "/igo/staging/GLP_pipeline/"
-COMMAND_PREFIX = "/opt/edico/bin/dragen -f -r /staging/ref/hg19"
+COMMAND_PREFIX = "/opt/edico/bin/dragen -f -r /igo/work/igo/dragen_hash_tables/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1"
 COMMAND_PARAMETER = "--enable-duplicate-marking true --enable-map-align true --enable-sv true --enable-map-align-output true --output-format bam --enable-variant-caller true --enable-hla true"
 FASTQ_PATH = "/igo/staging/FASTQ/"
 ENDPOINT = "https://igolims.mskcc.org:8443/LimsRest/getSamplePairs?igoSampleId="