AN-415 Eliminate reliance on test data from `gs://broad-public-datase…

…ts` (#7696)
broadinstitute · Feb 21, 2025 · 47bbf93 · 47bbf93
1 parent b2ecb61
commit 47bbf93
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Showing 4 changed files with 105 additions and 104 deletions.
diff --git a/...es/standardTestCases/reference_disk/gcpbatch_reference_disk_mounted_only_if_requested.wdl b/...es/standardTestCases/reference_disk/gcpbatch_reference_disk_mounted_only_if_requested.wdl
@@ -13,7 +13,7 @@ task MentionsNirvanaReference {
     input {
         # Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
         File mention =
-            "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
+            "gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
     }
     command <<<
         PS4='\D{+%F %T} \w $ '

diff --git a/...n/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl b/...n/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
@@ -13,7 +13,7 @@ task MentionsNirvanaReference {
     input {
         # Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
         File mention =
-            "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
+            "gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
     }
     command <<<
         PS4='\D{+%F %T} \w $ '

diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
@@ -1,5 +1,5 @@
 {
   "wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
-  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
-  "wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
+  "wf_reference_disk_test.nirvana_reference_file_input": "gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
+  "wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
 }
diff --git a/src/ci/resources/google_reference_image_manifest.conf b/src/ci/resources/google_reference_image_manifest.conf
@@ -191,156 +191,157 @@ reference-disk-localization-manifests = [
       }
     ]
   },
+  # Copied from Prod config `_cromwell-reference-images.conf.tpl` (WX-1505)
   {
-    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-02-01",
-    "diskSizeGb" : 55,
+    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2024-03-06-public-2024-03-12",
+    diskSizeGb: 55
     "files" : [ {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd",
-      "crc32c" : 1502286599
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/Cache/GRCh38/Both.polyphen.ndb"
+      crc32c: 3178180885
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
-      "crc32c" : 2106006282
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/Cache/GRCh38/Both.sift.ndb"
+      crc32c: 2786880382
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_gene_scores_2.1.nga",
-      "crc32c" : 3393536227
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/Cache/GRCh38/Both.transcripts.ndb"
+      crc32c: 2114520493
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa",
-      "crc32c" : 2371255414
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/References/Homo_sapiens.GRCh38.Nirvana.dat"
+      crc32c: 1694422311
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma.idx",
-      "crc32c" : 3985843783
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
+      crc32c: 2492681982
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/References/Homo_sapiens.GRCh38.Nirvana.dat",
-      "crc32c" : 1694422311
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa"
+      crc32c: 2371255414
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.sift.ndb",
-      "crc32c" : 2786880382
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa.idx"
+      crc32c: 870728029
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nsi",
-      "crc32c" : 3787486272
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma"
+      crc32c: 1696693985
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa",
-      "crc32c" : 3105778103
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma.idx"
+      crc32c: 3985843783
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa",
-      "crc32c" : 1821283507
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/COSMIC_GeneFusions_94.gfj"
+      crc32c: 429830169
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa",
-      "crc32c" : 1393836085
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_20160414.nsi"
+      crc32c: 1181611304
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa",
-      "crc32c" : 2730251112
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20231105.nga"
+      crc32c: 2121701417
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.transcripts.ndb",
-      "crc32c" : 2114520493
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20231105.nsi"
+      crc32c: 3746920330
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MultiZ100Way_20171006.pcs",
-      "crc32c" : 1251171842
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_disease_validity_curations_20231105.nga"
+      crc32c: 1696736207
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa.idx",
-      "crc32c" : 2183408606
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinVar_20231028.nsa"
+      crc32c: 1077441598
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-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa",
-      "crc32c" : 482110804
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinVar_20231028.nsa.idx"
+      crc32c: 1794906589
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa",
-      "crc32c" : 1654978963
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinVar_20231028.nsi"
+      crc32c: 622362682
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.polyphen.ndb",
-      "crc32c" : 3178180885
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa"
+      crc32c: 3457097933
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa.idx",
-      "crc32c" : 3807477399
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa.idx"
+      crc32c: 245207854
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_SV_2.1.nsi",
-      "crc32c" : 2600275374
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/DECIPHER_201509.nsi"
+      crc32c: 2426309371
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_disease_validity_curations_20220512.nga",
-      "crc32c" : 4116422668
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/FusionCatcher_1.33.gfs"
+      crc32c: 1420426876
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/OMIM_20220516.nga",
-      "crc32c" : 1767833806
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/GME_20160618.nsa"
+      crc32c: 1210977352
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+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/GME_20160618.nsa.idx"
+      crc32c: 1732177354
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-      "crc32c" : 1732177354
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa"
+      crc32c: 2730251112
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-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa.idx",
-      "crc32c" : 245207854
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa.idx"
+      crc32c: 3139541733
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-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa",
-      "crc32c" : 4136875677
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa"
+      crc32c: 1721491427
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsi",
-      "crc32c" : 1056818502
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
+      crc32c: 2375984948
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-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa",
-      "crc32c" : 1210977352
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_SV_20200819.nsi"
+      crc32c: 1378887803
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa.idx",
-      "crc32c" : 870728029
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MultiZ100Way_20171006.pcs"
+      crc32c: 1251171842
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_LCR_2.1.lcr",
-      "crc32c" : 3602069872
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/OMIM_20220516.nga"
+      crc32c: 1767833806
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa.idx",
-      "crc32c" : 2835194789
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa"
+      crc32c: 4136875677
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nga",
-      "crc32c" : 2485206803
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa.idx"
+      crc32c: 2835194789
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_SV_20200819.nsi",
-      "crc32c" : 1378887803
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa"
+      crc32c: 710316739
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa.idx",
-      "crc32c" : 302652747
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa.idx"
+      crc32c: 302652747
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_20160414.nsi",
-      "crc32c" : 1181611304
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa"
+      crc32c: 3105778103
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+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa.idx"
+      crc32c: 980438557
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DECIPHER_201509.nsi",
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+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa"
+      crc32c: 1393836085
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-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa",
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+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa.idx"
+      crc32c: 3807477399
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-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa.idx",
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+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa"
+      crc32c: 1821283507
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/COSMIC_GeneFusions_94.gfj",
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+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa.idx"
+      crc32c: 37093822
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-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa.idx",
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+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/dbSNP_156.nsa"
+      crc32c: 579363434
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/FusionCatcher_1.33.gfs",
-      "crc32c" : 1420426876
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/dbSNP_156.nsa.idx"
+      crc32c: 1758636340
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi",
-      "crc32c" : 2492681982
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa"
+      crc32c: 4247114985
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx",
-      "crc32c" : 2375984948
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa.idx"
+      crc32c: 3582543830
     }, {
-      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa.idx",
-      "crc32c" : 1539516090
+      path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/gnomAD_LCR_2.1.lcr"
+      crc32c: 3602069872
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