Beta is the new Unified

.dockstore.yml

@@ -171,13 +171,6 @@ workflows:
        branches:
          - master
          - ah_var_store
-   - name: GvsUnified
-     subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsUnified.wdl
-     filters:
-       branches:
-         - master
-         - ah_var_store
    - name: GvsJointVariantCalling
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl

scripts/variantstore/wdl/GvsJointVariantCalling.wdl

@@ -1,6 +1,10 @@
 version 1.0
 
-import "GvsUnified.wdl" as GvsUnified
+import "GvsBulkIngestGenomes.wdl" as BulkIngestGenomes
+import "GvsPopulateAltAllele.wdl" as PopulateAltAllele
+import "GvsCreateFilterSet.wdl" as CreateFilterSet
+import "GvsPrepareRangesCallset.wdl" as PrepareRangesCallset
+import "GvsExtractCallset.wdl" as ExtractCallset
 
 workflow GvsJointVariantCalling {
     input {
@@ -29,6 +33,12 @@ workflow GvsJointVariantCalling {
     String extract_output_file_base_name = sub(call_set_identifier, "\\s+|\_+", "-")
     String extract_table_prefix = sub(call_set_identifier, "\\s+|\_+", "-")
     String filter_set_name = sub(call_set_identifier, "\\s+|\_+", "-")
+
+    String query_project = project_id
+    String destination_project = project_id
+    String destination_dataset = dataset_name
+    String fq_temp_table_dataset = "~{destination_project}.~{destination_dataset}"
+
     if (false) {
       Int extract_maxretries_override = ""
       Int extract_preemptible_override = ""
@@ -48,53 +58,89 @@ workflow GvsJointVariantCalling {
 
     File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
 
-    call GvsUnified.GvsUnified {
+
+    call BulkIngestGenomes.GvsBulkIngestGenomes as BulkIngestGenomes {
+        input:
+            dataset_name = dataset_name,
+            project_id = project_id,
+            gatk_override = gatk_override,
+            interval_list = interval_list,
+            drop_state = drop_state,
+            sample_id_column_name = sample_id_column_name,
+            vcf_files_column_name = vcf_files_column_name,
+            vcf_index_files_column_name = vcf_index_files_column_name,
+            sample_set_name = sample_set_name,
+    }
+
+    call PopulateAltAllele.GvsPopulateAltAllele {
         input:
             call_set_identifier = call_set_identifier,
+            go = BulkIngestGenomes.done,
             dataset_name = dataset_name,
             project_id = project_id,
+    }
+
+    call CreateFilterSet.GvsCreateFilterSet {
+        input:
+            go = GvsPopulateAltAllele.done,
+            dataset_name = dataset_name,
+            project_id = project_id,
+            call_set_identifier = call_set_identifier,
             filter_set_name = filter_set_name,
-            use_VQSR_lite = !use_classic_VQSR,
-            extract_output_gcs_dir = extract_output_gcs_dir,
-            destination_dataset = dataset_name,
-            destination_project = project_id,
-            extract_do_not_filter_override = extract_do_not_filter_override,
-            extract_maxretries_override = extract_maxretries_override,
-            extract_output_file_base_name = extract_output_file_base_name,
-            extract_preemptible_override = extract_preemptible_override,
-            extract_scatter_count = extract_scatter_count,
-            extract_table_prefix = extract_table_prefix,
-            fq_temp_table_dataset = "~{project_id}.~{dataset_name}",
-            gatk_override = gatk_override,
+            use_VQSR_lite = use_classic_VQSR,
             interval_list = interval_list,
-            interval_weights_bed = interval_weights_bed,
-            load_data_batch_size = load_data_batch_size,
-            load_data_maxretries_override = load_data_maxretries_override,
-            load_data_preemptible_override = load_data_preemptible_override,
-            query_labels = query_labels,
-            query_project = project_id,
-            sample_names_to_extract = sample_names_to_extract,
-            split_intervals_disk_size_override = split_intervals_disk_size_override,
-            split_intervals_mem_override = split_intervals_mem_override,
+            gatk_override = gatk_override,
             INDEL_VQSR_CLASSIC_max_gaussians_override = INDEL_VQSR_CLASSIC_max_gaussians_override,
             INDEL_VQSR_CLASSIC_mem_gb_override = INDEL_VQSR_CLASSIC_mem_gb_override,
             SNP_VQSR_CLASSIC_max_gaussians_override = SNP_VQSR_CLASSIC_max_gaussians_override,
             SNP_VQSR_CLASSIC_mem_gb_override = SNP_VQSR_CLASSIC_mem_gb_override,
+    }
+
+    call PrepareRangesCallset.GvsPrepareCallset {
+        input:
+            call_set_identifier = call_set_identifier,
+            go = GvsCreateFilterSet.done,
+            dataset_name = dataset_name,
+            project_id = project_id,
+            extract_table_prefix = extract_table_prefix,
+            query_project = query_project,
+            destination_project = destination_project,
+            destination_dataset = destination_dataset,
+            fq_temp_table_dataset = fq_temp_table_dataset,
+            query_labels = query_labels,
+            sample_names_to_extract = sample_names_to_extract,
+    }
+
+    call ExtractCallset.GvsExtractCallset {
+        input:
+            go = GvsPrepareCallset.done,
+            dataset_name = dataset_name,
+            project_id = project_id,
+            call_set_identifier = call_set_identifier,
+            extract_table_prefix = extract_table_prefix,
+            filter_set_name = filter_set_name,
+            query_project = query_project,
+            scatter_count = extract_scatter_count,
+            interval_list = interval_list,
+            interval_weights_bed = interval_weights_bed,
+            gatk_override = gatk_override,
+            output_file_base_name = extract_output_file_base_name,
+            extract_maxretries_override = extract_maxretries_override,
+            extract_preemptible_override = extract_preemptible_override,
+            output_gcs_dir = extract_output_gcs_dir,
+            split_intervals_disk_size_override = split_intervals_disk_size_override,
+            split_intervals_mem_override = split_intervals_mem_override,
+            do_not_filter_override = extract_do_not_filter_override,
             drop_state = drop_state,
-            is_beta_user = tighter_gcp_quotas,
-            sample_id_column_name = sample_id_column_name,
-            vcf_files_column_name = vcf_files_column_name,
-            vcf_index_files_column_name = vcf_index_files_column_name,
-            sample_set_name = sample_set_name,
     }
 
     output {
-        Array[File] output_vcfs = GvsUnified.output_vcfs
-        Array[File] output_vcf_indexes = GvsUnified.output_vcf_indexes
-        Array[File] output_vcf_interval_files = GvsUnified.output_vcf_interval_files
-        Float total_vcfs_size_mb = GvsUnified.total_vcfs_size_mb
-        File? sample_name_list = GvsUnified.sample_name_list
-        File manifest = GvsUnified.manifest
+        Array[File] output_vcfs = GvsExtractCallset.output_vcfs
+        Array[File] output_vcf_indexes = GvsExtractCallset.output_vcf_indexes
+        Array[File] output_vcf_interval_files = GvsExtractCallset.output_vcf_interval_files
+        Float total_vcfs_size_mb = GvsExtractCallset.total_vcfs_size_mb
+        File? sample_name_list = GvsExtractCallset.sample_name_list
+        File manifest = GvsExtractCallset.manifest
         Boolean done = true
     }
 }

scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl

@@ -1,6 +1,5 @@
 version 1.0
 
-import "GvsUnified.wdl" as Unified
 import "GvsUtils.wdl" as Utils
 import "GvsJointVariantCalling.wdl" as JointVariantCalling