diff --git a/datalake-spark3/src/main/resources/reference_kf.conf b/datalake-spark3/src/main/resources/reference_kf.conf index d3e31326..ef87484b 100644 --- a/datalake-spark3/src/main/resources/reference_kf.conf +++ b/datalake-spark3/src/main/resources/reference_kf.conf @@ -43,16 +43,16 @@ datalake { }, { format=VCF - id="raw_gnomad_genomes_v4" + id="raw_gnomad_genomes_v3" keys=[] loadtype=OverWrite partitionby=[] - path="/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr[^M]*.vcf.bgz" + path="/release/3.1/vcf/genomes/gnomad.genomes.v3.1.sites.chr[^M]*.vcf.bgz" readoptions { flattenInfoFields="true" "split_multiallelics"="true" } - storageid=gnomadv4 + storageid=gnomad writeoptions { "created_on_column"="created_on" "is_current_column"="is_current" @@ -63,11 +63,11 @@ datalake { }, { format=VCF - id="raw_gnomad_genomes_v3" + id="raw_gnomad_genomes_v4" keys=[] loadtype=OverWrite partitionby=[] - path="/release/3.1/vcf/genomes/gnomad.genomes.v3.1.sites.chr[^M]*.vcf.bgz" + path="/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr[^M]*.vcf.bgz" readoptions { flattenInfoFields="true" "split_multiallelics"="true" @@ -880,7 +880,7 @@ datalake { partitionby=[ chromosome ] - path="/public/gnomad_genomes_4" + path="/public/gnomad_genomes_v4" readoptions {} storageid="public_database" table { diff --git a/datalake-spark3/src/test/resources/config/reference_kf.conf b/datalake-spark3/src/test/resources/config/reference_kf.conf index 88cb559a..ef87484b 100644 --- a/datalake-spark3/src/test/resources/config/reference_kf.conf +++ b/datalake-spark3/src/test/resources/config/reference_kf.conf @@ -43,16 +43,16 @@ datalake { }, { format=VCF - id="raw_gnomad_genomes_v4" + id="raw_gnomad_genomes_v3" keys=[] loadtype=OverWrite partitionby=[] - path="/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr[^M]*.vcf.bgz" + path="/release/3.1/vcf/genomes/gnomad.genomes.v3.1.sites.chr[^M]*.vcf.bgz" readoptions { flattenInfoFields="true" "split_multiallelics"="true" } - storageid=gnomadv4 + storageid=gnomad writeoptions { "created_on_column"="created_on" "is_current_column"="is_current" @@ -63,11 +63,11 @@ datalake { }, { format=VCF - id="raw_gnomad_genomes_v3" + id="raw_gnomad_genomes_v4" keys=[] loadtype=OverWrite partitionby=[] - path="/release/3.1/vcf/genomes/gnomad.genomes.v3.1.sites.chr[^M]*.vcf.bgz" + path="/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr[^M]*.vcf.bgz" readoptions { flattenInfoFields="true" "split_multiallelics"="true" @@ -885,7 +885,7 @@ datalake { storageid="public_database" table { database=variant - name="gnomad_genomes_v3" + name="gnomad_genomes_v4" } view { database="variant_live" @@ -898,7 +898,7 @@ datalake { "valid_from_column"="valid_from" "valid_to_column"="valid_to" } - } + }, { format=DELTA id="normalized_human_genes"