Remove hard-coded db table path.

broadinstitute · May 16, 2022 · 83ac402 · 83ac402
1 parent 0ff2f76
commit 83ac402
Showing 1 changed file with 10 additions and 10 deletions.
diff --git a/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl b/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl
@@ -959,7 +959,7 @@ task SchemaAAChangeAndExonNumberConsistent {
         COUNT (DISTINCT vid) AS count FROM
         (
             SELECT vid
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE exon_number IS NULL
             AND aa_change IS NOT NULL
             AND NOT (("intron_variant" IN UNNEST(consequence) AND (variant_type IN ("insertion", "deletion"))))
@@ -970,7 +970,7 @@ task SchemaAAChangeAndExonNumberConsistent {
             AND "coding_sequence_variant" NOT IN UNNEST(consequence)
         UNION DISTINCT
             SELECT vid
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE exon_number IS NOT NULL
             AND aa_change IS NULL
             AND "non_coding_transcript_exon_variant" NOT IN UNNEST(consequence)
@@ -1059,47 +1059,47 @@ task SpotCheckForAAChangeAndExonNumberConsistency {
         COUNT (DISTINCT vid) FROM
         (
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "12-42446055-C-CGACCCTGCA" AND transcript = "ENST00000610488.4" AND exon_number IS NULL
             AND aa_change = "ENSP00000479913.1:p.(Ser375_Ala376insThrLeuGln)" AND "intron_variant" IN UNNEST(consequence) AND variant_type = "insertion"
             -- Another insertion
         UNION ALL
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "16-29810099-G-GGCGGCGGCAGCGGCA" AND transcript = "ENST00000566906.6" AND exon_number IS NULL
             AND aa_change = "ENSP00000461174.1:p.(Gly95_Ser99dup)" AND "intron_variant" IN UNNEST(consequence) AND variant_type = "insertion"
         UNION ALL
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "7-114631524-CCAG-C" AND transcript = "ENST00000393495.7" AND exon_number IS NULL
             AND aa_change = "ENSP00000377133.3:p.(Gln63del)" AND "intron_variant" IN UNNEST(consequence) AND variant_type = "deletion"
             --another
         UNION ALL
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "7-23198205-CTTTTTTT-C" and transcript = "ENST00000548367.2" AND exon_number IS NULL
             AND aa_change = "ENSP00000482736.1:p.(Phe25Ter)" AND "intron_variant" IN UNNEST(consequence) AND variant_type = "deletion"
         UNION ALL
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "1-40060064-T-TA" AND transcript = "ENST00000449311.5"
             AND exon_number IS NULL AND aa_change IS NULL
             AND "intron_variant" IN UNNEST(consequence) AND variant_type = "insertion"
         UNION ALL
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "17-1483061-T-TG" AND transcript = "ENST00000574790.5"
             AND exon_number IS NULL AND aa_change IS NULL
             AND "intron_variant" IN UNNEST(consequence) AND variant_type = "insertion"
         UNION ALL
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "1-46560284-TG-T" AND transcript = "ENST00000371945.8"
             AND exon_number IS NULL AND aa_change IS NULL
             AND "intron_variant" IN UNNEST(consequence) AND variant_type = "deletion"
         UNION ALL
             SELECT vid, transcript, exon_number, aa_change, consequence, variant_type
-            FROM `aou-genomics-curation-prod.beta2_99k.vat_v3`
+            FROM ~{fq_vat_table}
             WHERE vid = "6-111741100-CA-C" AND transcript = "ENST00000518295.5"
             AND exon_number IS NULL AND aa_change IS NULL
             AND "intron_variant" IN UNNEST(consequence) AND variant_type = "deletion"