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Sample chromosome ploidy support for RWB Echo [VS-1500] #9051

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Sample chromosome ploidy support for RWB Echo [VS-1500] #9051

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c635e1d
Echo sample_chromosome_ploidy schema updates for AoU RWB [VS-1500]
mcovarr Nov 19, 2024
573e420
wip
mcovarr Nov 20, 2024
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6 changes: 5 additions & 1 deletion scripts/variantstore/wdl/GvsAssignIds.wdl
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Expand Up @@ -28,7 +28,11 @@ workflow GvsAssignIds {
String vcf_header_lines_schema_json = '[{"name":"vcf_header_lines_hash","type":"STRING","mode":"REQUIRED"}, {"name":"vcf_header_lines","type":"STRING","mode":"REQUIRED"},{"name":"is_expected_unique","type":"BOOLEAN","mode":"REQUIRED"}]'
String sample_vcf_header_schema_json = '[{"name": "sample_id","type": "INTEGER","mode": "REQUIRED"}, {"name":"vcf_header_lines_hash","type":"STRING","mode":"REQUIRED"}]'
String sample_load_status_schema_json = '[{"name": "sample_id","type": "INTEGER","mode": "REQUIRED"},{"name":"status","type":"STRING","mode":"REQUIRED"}, {"name":"event_timestamp","type":"TIMESTAMP","mode":"REQUIRED"}]'
String sample_chromosome_ploidy_schema_json = '[{"name": "sample_id","type": "INTEGER","mode": "REQUIRED"},{"name": "chromosome","type": "INTEGER","mode": "REQUIRED"},{"name": "ploidy","type": "INTEGER","mode": "REQUIRED"}]'
# The schema below for the `sample_chromosome_ploidy` table matches that in the AoU `echo` dataset, which differs from
# the standard `sample_chromosome_ploidy` schema by the addition of the `genotype` column. At the time of this writing
# it is not expected that any additional samples will be loaded into the `echo` dataset, but if there are additional
# samples then this code will match the actual `echo` schema.
String sample_chromosome_ploidy_schema_json = '[{"name": "sample_id","type": "INTEGER","mode": "REQUIRED"},{"name": "chromosome","type": "INTEGER","mode": "REQUIRED"},{"name":"genotype","type":"STRING","mode":"NULLABLE"},{"name": "ploidy","type": "INTEGER","mode": "REQUIRED"}]'
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These changes aren't actually necessary for supporting RWB extract. They likely won't hurt, but they are not necessary for this PR as RWB does not run this wdl.

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Yeah that's kinda what I was trying to say with the comment. 🙂 It was bugging me that this was out of sync with SchemaUtils.java, even if we're super unlikely to ever need these changes.


if (!defined(git_hash) || !defined(cloud_sdk_docker)) {
call Utils.GetToolVersions {
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsUtils.wdl
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Expand Up @@ -74,7 +74,7 @@ task GetToolVersions {
String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim"
String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2024-11-05-alpine-a55d2253d280"
String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024-10-24-gatkbase-b29b46ab0443"
String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024-11-19-gatkbase-b01d93162302"
String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"
String gotc_imputation_docker = "us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.5-1.10.2-0.1.16-1649948623"
String plink_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/plink2:2024-04-23-slim-a0a65f52cc0e"
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/gvs/common/SchemaUtils.java
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Expand Up @@ -79,7 +79,7 @@ public class SchemaUtils {
CALL_PGT, CALL_PID, CALL_PS);


public static final List<String> SAMPLE_PLOIDY_FIELDS = Arrays.asList(CHROMOSOME, SAMPLE_ID, PLOIDY);
public static final List<String> SAMPLE_PLOIDY_FIELDS = Arrays.asList(CHROMOSOME, SAMPLE_ID, GENOTYPE, PLOIDY);

public static final List<String> EXTRACT_REF_FIELDS = Arrays.asList(LOCATION_FIELD_NAME, SAMPLE_ID_FIELD_NAME, LENGTH_FIELD_NAME, STATE_FIELD_NAME);

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