feat: CLIN-3562 fix test for external_frequencies

Ferlab-Ste-Justine · Jan 16, 2025 · a08583f · a08583f
1 parent 79dc1cd
commit a08583f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/datalake-spark3/src/main/scala/bio/ferlab/datalake/spark3/genomics/enriched/Variants.scala b/datalake-spark3/src/main/scala/bio/ferlab/datalake/spark3/genomics/enriched/Variants.scala
@@ -132,7 +132,7 @@ object Variants {
       val conditionValueMap: List[(Column, String)] = List(
         $"clinvar".isNotNull -> "Clinvar",
         $"cmc".isNotNull -> "Cosmic",
-        $"external_frequencies".isNotNull -> "gnomADv4",
+        $"external_frequencies.gnomad_genomes_4".isNotNull -> "gnomADv4",
       )
       val dfWithVariantExternalReference = conditionValueMap.foldLeft {
         df.withColumn(outputColumn, when($"rsnumber".isNotNull, array(lit("DBSNP"))).otherwise(array()))