Azurized wdls

pipelines/broad/arrays/imputation/Imputation.changelog.md

@@ -1,3 +1,9 @@
+# 1.1.13
+2023-05-21 (Date of Last Commit)
+
+* Updated GermlineVariantDiscovery, BamProcessing, DragenTasks, Qc, and Utilities tasks to allow multi-cloud dockers. This change does not affect this pipeline.
+
+
 # 1.1.12
 2023-12-18 (Date of Last Commit)
 

pipelines/broad/arrays/imputation/Imputation.wdl

@@ -6,7 +6,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Imputation {
 
-  String pipeline_version = "1.1.12"
+  String pipeline_version = "1.1.13"
 
   input {
     Int chunkLength = 25000000

pipelines/broad/arrays/single_sample/Arrays.changelog.md

@@ -1,3 +1,7 @@
+# 2.6.25
+2024-07-09
+* Updated tasks GermlineVariantDiscovery.wdl and QC.wdl to allow multi-cloud dockers; this does not affect this pipeline.
+
 # 2.6.24
 2024-07-01 (Date of Last Commit)
 

pipelines/broad/arrays/single_sample/Arrays.wdl

@@ -23,7 +23,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Arrays {
 
-  String pipeline_version = "2.6.24"
+  String pipeline_version = "2.6.25"
 
   input {
     String chip_well_barcode

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md

@@ -1,3 +1,8 @@
+# 2.1.14
+2024-07-09 (Date of Last Commit)
+
+* Updated ReblockGVCF.wdl to run in Azure.
+
 # 2.1.13
 2024-07-01 (Date of Last Commit)
 

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.exome.inputs.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/ExomeGermlineSingleSample/truth/plumbing/master/RP-929.NA12878/NA12878_PLUMBING.rb.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider":"gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl

@@ -2,10 +2,11 @@ version 1.0
 
 import "../../../../../../tasks/broad/GermlineVariantDiscovery.wdl" as Calling
 import "../../../../../../tasks/broad/Qc.wdl" as QC
+import "../../../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow ReblockGVCF {
 
-  String pipeline_version = "2.1.13"
+  String pipeline_version = "2.1.14"
 
 
   input {
@@ -20,9 +21,22 @@ workflow ReblockGVCF {
     String? annotations_to_remove_command
     Boolean? move_filters_to_genotypes
     String gvcf_file_extension = ".g.vcf.gz"
+    String cloud_provider
   }
 
   String gvcf_basename = basename(gvcf, gvcf_file_extension)
+  # docker images
+  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
+  String gatk_docker_azure = "dsppipelinedev.azurecr.io/gatk_reduced_layers:latest"
+  String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure
+
+  # make sure either gcp or azr is supplied as cloud_provider input
+  if ((cloud_provider != "gcp") && (cloud_provider != "azure")) {
+    call utils.ErrorWithMessage as ErrorMessageIncorrectInput {
+      input:
+        message = "cloud_provider must be supplied with either 'gcp' or 'azure'."
+    }
+  }
 
   call Calling.Reblock as Reblock {
     input:
@@ -35,7 +49,8 @@ workflow ReblockGVCF {
       annotations_to_keep_command = annotations_to_keep_command,
       annotations_to_remove_command = annotations_to_remove_command,
       move_filters_to_genotypes = move_filters_to_genotypes,
-      output_vcf_filename = gvcf_basename + ".rb.g.vcf.gz"
+      output_vcf_filename = gvcf_basename + ".rb.g.vcf.gz",
+      docker_path = gatk_docker
   }
 
     # Validate the (g)VCF output of HaplotypeCaller
@@ -51,7 +66,7 @@ workflow ReblockGVCF {
         calling_intervals_defined = defined(calling_interval_list),
         is_gvcf = true,
         extra_args = "--no-overlaps",
-        gatk_docker = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
+        docker_path = gatk_docker
     }
 
   output {

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Plumbing/G96830.NA12878.index.json

@@ -3,6 +3,7 @@
     "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/wgs/plumbing/input/G96830.NA12878/index_in_different_location/NA12878_PLUMBING.g.vcf.gz.tbi",
     "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
     "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-    "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+    "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+    "ReblockGVCF.cloud_provider": "gcp"
   }
 

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Plumbing/G96830.NA12878.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Plumbing/NA12878.ultima.json

@@ -6,5 +6,6 @@
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
   "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "ReblockGVCF.tree_score_cutoff": 0.2,
-  "ReblockGVCF.annotations_to_keep_command": "--annotations-to-keep TREE_SCORE --annotations-to-keep ASSEMBLED_HAPS --annotations-to-keep FILTERED_HAPS"
+  "ReblockGVCF.annotations_to_keep_command": "--annotations-to-keep TREE_SCORE --annotations-to-keep ASSEMBLED_HAPS --annotations-to-keep FILTERED_HAPS",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Plumbing/RP-929.NA12878.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/plumbing/input/RP-929.NA12878/NA12878_PLUMBING.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/C1963.CHMI_CHMI3_Nex1/CHMI_CHMI3_Nex1.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/C862.NA19238.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/C862.NA19238/NA19238.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/D5327.NA12878.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/D5327.NA12878/NA12878.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/D5327.NA12891.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/D5327.NA12891/NA12891.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/G94794.CHMI_CHMI3_WGS2.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/G94982.NA12878.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/G94982.NA12891.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/G94982.NA12892.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/G96830.NA12878.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/NA12878.bge.json

@@ -7,5 +7,6 @@
   "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "ReblockGVCF.annotations_to_remove_command": "--format-annotations-to-remove PRI",
   "ReblockGVCF.move_filters_to_genotypes": true,
-  "ReblockGVCF.gvcf_file_extension": ".gvcf.gz"
+  "ReblockGVCF.gvcf_file_extension": ".gvcf.gz",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/NA12878.ultima.json

@@ -6,5 +6,6 @@
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
   "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "ReblockGVCF.tree_score_cutoff": 0.2,
-  "ReblockGVCF.annotations_to_keep_command": "--annotations-to-keep TREE_SCORE --annotations-to-keep ASSEMBLED_HAPS --annotations-to-keep FILTERED_HAPS"
+  "ReblockGVCF.annotations_to_keep_command": "--annotations-to-keep TREE_SCORE --annotations-to-keep ASSEMBLED_HAPS --annotations-to-keep FILTERED_HAPS",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/RP-1535.NA17-308.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/RP-1535.NA17-308/NA17-308.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/RP-518.NA12878.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/exome/Plumbing/RP-929.NA12878.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/plumbing/input/RP-929.NA12878/NA12878_PLUMBING.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/exome/Scientific/C1963.CHMI_CHMI3_Nex1.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/C1963.CHMI_CHMI3_Nex1/CHMI_CHMI3_Nex1.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/exome/Scientific/C862.NA19238.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/C862.NA19238/NA19238.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/exome/Scientific/D5327.NA12878.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/D5327.NA12878/NA12878.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/exome/Scientific/D5327.NA12891.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/D5327.NA12891/NA12891.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/exome/Scientific/D5327.NA12892.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/D5327.NA12892/NA12892.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/exome/Scientific/RP-1535.NA17-308.json

@@ -3,5 +3,6 @@
   "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/reblock_gvcf/exome/scientific/input/RP-1535.NA17-308/NA17-308.g.vcf.gz.tbi",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/wgs/Plumbing/G96830.NA12878.json

@@ -4,5 +4,6 @@
   "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
   "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.cloud_provider": "gcp"
 }

pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/test_inputs/wgs/Plumbing/NA12878.ultima.json

@@ -6,5 +6,6 @@
   "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
   "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "ReblockGVCF.tree_score_cutoff": 0.2,
-  "ReblockGVCF.annotations_to_keep_command": "--annotations-to-keep TREE_SCORE --annotations-to-keep ASSEMBLED_HAPS --annotations-to-keep FILTERED_HAPS"
+  "ReblockGVCF.annotations_to_keep_command": "--annotations-to-keep TREE_SCORE --annotations-to-keep ASSEMBLED_HAPS --annotations-to-keep FILTERED_HAPS",
+  "ReblockGVCF.cloud_provider": "gcp"
 }