From 7bbf4d3f24e6fbf630005e191570088e8a7f88b4 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Mon, 24 Oct 2022 17:26:14 -0400
Subject: [PATCH 01/49] wip

---
 .dockstore.yml                                |   8 +
 .../wdl/GvsExtractAvroFilesForHail.wdl        |   1 +
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   | 144 ++++++++++++++++++
 3 files changed, 153 insertions(+)
 create mode 100644 scripts/variantstore/wdl/GvsUnifiedHail.wdl

diff --git a/.dockstore.yml b/.dockstore.yml
index 87060478101..0ada2e8f73f 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -180,6 +180,14 @@ workflows:
        branches:
          - master
          - ah_var_store
+   - name: GvsUnifiedHail
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsUnifiedHail.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - vs_639_hail_testing_spike
    - name: GvsJointVariantCalling
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl
diff --git a/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl b/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
index 7105dc07f9b..b1d780bd1b3 100644
--- a/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
+++ b/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
@@ -5,6 +5,7 @@ import "GvsUtils.wdl" as Utils
 
 workflow GvsExtractAvroFilesForHail {
     input {
+        Boolean go = true
         String project_id
         String dataset
         String filter_set_name
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
new file mode 100644
index 00000000000..5bac773b82c
--- /dev/null
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -0,0 +1,144 @@
+version 1.0
+
+import "GvsAssignIds.wdl" as AssignIds
+import "GvsImportGenomes.wdl" as ImportGenomes
+import "GvsPopulateAltAllele.wdl" as PopulateAltAllele
+import "GvsCreateFilterSet.wdl" as CreateFilterSet
+import "GvsExtractAvroFilesForHail.wdl" as ExtractAvroFilesForHail
+
+workflow GvsUnifiedHail {
+    input {
+        # Begin GvsAssignIds
+        String dataset_name
+        String project_id
+        String call_set_identifier
+
+        Array[String] external_sample_names
+        String call_set_identifier
+
+        File? gatk_override
+        # End GvsAssignIds
+
+        # Begin GvsImportGenomes
+        Array[File] input_vcfs
+        Array[File] input_vcf_indexes
+        File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
+
+        # set to "NONE" to ingest all the reference data into GVS for VDS (instead of VCF) output
+        String drop_state = "NONE"
+
+        # The larger the `load_data_batch_size` the greater the probability of preemptions and non-retryable
+        # BigQuery errors so if specifying this adjust preemptible and maxretries accordingly. Or just take the defaults,
+        # those should work fine in most cases.
+        Int? load_data_batch_size
+        Int? load_data_preemptible_override
+        Int? load_data_maxretries_override
+        # End GvsImportGenomes
+
+        # Begin GvsCreateFilterSet
+        String filter_set_name = call_set_identifier
+        Array[String] indel_recalibration_annotation_values = ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"]
+        Array[String] snp_recalibration_annotation_values = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"]
+
+        Int? INDEL_VQSR_max_gaussians_override = 4
+        Int? INDEL_VQSR_mem_gb_override
+        Int? SNP_VQSR_max_gaussians_override = 6
+        Int? SNP_VQSR_mem_gb_override
+        # End GvsCreateFilterSet
+
+        # Begin CreateVds
+        File hail_wheel = "gs://gvs-internal-scratch/hail-wheels/2022-10-18/0.2.102-964bee061eb0/hail-0.2.102-py3-none-any.whl"
+        # End CreateVds
+    }
+
+    call AssignIds.GvsAssignIds as AssignIds {
+        input:
+            dataset_name = dataset_name,
+            project_id = project_id,
+            external_sample_names = external_sample_names,
+            assign_ids_gatk_override = gatk_override
+    }
+
+    call ImportGenomes.GvsImportGenomes {
+        input:
+            go = AssignIds.done,
+            dataset_name = dataset_name,
+            project_id = project_id,
+            external_sample_names = external_sample_names,
+            input_vcfs = input_vcfs,
+            input_vcf_indexes = input_vcf_indexes,
+            interval_list = interval_list,
+            load_data_preemptible_override = load_data_preemptible_override,
+            load_data_maxretries_override = load_data_maxretries_override,
+            load_data_gatk_override = gatk_override,
+            load_data_batch_size = load_data_batch_size,
+            drop_state = drop_state
+    }
+
+    call PopulateAltAllele.GvsPopulateAltAllele {
+        input:
+            call_set_identifier = call_set_identifier,
+            go = GvsImportGenomes.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,
+            indel_recalibration_annotation_values = indel_recalibration_annotation_values,
+            snp_recalibration_annotation_values = snp_recalibration_annotation_values,
+            interval_list = interval_list,
+            gatk_override = gatk_override,
+            INDEL_VQSR_max_gaussians_override = INDEL_VQSR_max_gaussians_override,
+            INDEL_VQSR_mem_gb_override = INDEL_VQSR_mem_gb_override,
+            SNP_VQSR_max_gaussians_override = SNP_VQSR_max_gaussians_override,
+            SNP_VQSR_mem_gb_override = SNP_VQSR_mem_gb_override
+    }
+
+    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
+        input:
+            go = GvsCreateFilterSet.done,
+            project_id = project_id,
+            dataset = dataset_name,
+            filter_set_name = filter_set_name,
+            scatter_width = 10,
+    }
+
+    call CreateVds {
+        input:
+            hail_gvs_import_script = GvsExtractAvroFilesForHail.hail_gvs_import_script,
+            hail_wheel = hail_wheel,
+    }
+
+    output {
+        Boolean done = true
+    }
+}
+
+task CreateVds {
+    input {
+        File hail_gvs_import_script
+        File hail_wheel
+    }
+    command <<<
+        # Prepend date, time and pwd to xtrace log entries.
+        PS4='\D{+%F %T} \w $ '
+        set -o errexit -o nounset -o pipefail -o xtrace
+
+        pip install ~{hail_wheel}
+        python3 ~{hail_gvs_import_script}
+    >>>
+    runtime {
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-24-alpine"
+        disks: "local-disk 500 HDD"
+        cpu: 8
+    }
+    output {
+        Boolean done = true
+    }
+}

From 7fc099bc1c2c19dcf6c5f2dde0bf1c3b5e0e7e35 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Mon, 24 Oct 2022 17:35:44 -0400
Subject: [PATCH 02/49] integration

---
 .dockstore.yml                                |   9 +-
 .../wdl/GvsQuickstartHailIntegration.wdl      | 336 ++++++++++++++++++
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   |   1 +
 3 files changed, 345 insertions(+), 1 deletion(-)
 create mode 100644 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl

diff --git a/.dockstore.yml b/.dockstore.yml
index 0ada2e8f73f..00407d8647b 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -216,7 +216,14 @@ workflows:
        branches:
          - master
          - ah_var_store
-         - vs_707_azure_setup
+   - name: GvsQuickstartHailIntegration
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - vs_639_hail_testing_spike
    - name: GvsIngestTieout
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
new file mode 100644
index 00000000000..9140384dea7
--- /dev/null
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -0,0 +1,336 @@
+version 1.0
+
+import "GvsUnifiedHail.wdl" as Unified
+import "GvsUtils.wdl" as Utils
+
+workflow GvsQuickstartHailIntegration {
+
+    input {
+        String branch_name
+        String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-07-05/"
+
+        Array[String] external_sample_names = [
+                                              "ERS4367795",
+                                              "ERS4367796",
+                                              "ERS4367797",
+                                              "ERS4367798",
+                                              "ERS4367799",
+                                              "ERS4367800",
+                                              "ERS4367801",
+                                              "ERS4367803",
+                                              "ERS4367804",
+                                              "ERS4367805"
+                                              ]
+
+        Array[File] input_vcfs = [
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz"
+                                 ]
+
+        Array[File] input_vcf_indexes = [
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi"
+                                        ]
+
+        String drop_state = "FORTY"
+    }
+    String project_id = "gvs-internal"
+
+    call Utils.BuildGATKJarAndCreateDataset {
+        input:
+            branch_name = branch_name,
+            dataset_prefix = "quickit"
+    }
+
+    call Unified.GvsUnifiedHail {
+        input:
+            call_set_identifier = branch_name,
+            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+            project_id = project_id,
+            external_sample_names = external_sample_names,
+            gatk_override = BuildGATKJarAndCreateDataset.jar,
+            input_vcfs = input_vcfs,
+            input_vcf_indexes = input_vcf_indexes,
+            filter_set_name = "quickit",
+            drop_state = drop_state
+    }
+
+#    call AssertIdenticalOutputs {
+#        input:
+#            expected_output_prefix = expected_output_prefix,
+#            actual_vcfs = GvsUnified.output_vcfs
+#    }
+#
+#    call AssertCostIsTrackedAndExpected {
+#        input:
+#            go = GvsUnified.done,
+#            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+#            project_id = project_id,
+#            expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
+#    }
+#
+#    call AssertTableSizesAreExpected {
+#        input:
+#            go = GvsUnified.done,
+#            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+#            project_id = project_id,
+#            expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
+#    }
+#
+    output {
+        String vds_output_path = GvsUnifiedHail.vds_output_path
+        Boolean done = true
+    }
+}
+
+
+task AssertIdenticalOutputs {
+    input {
+        String expected_output_prefix
+        Array[File] actual_vcfs
+    }
+
+    command <<<
+        set -o errexit
+        set -o nounset
+        set -o pipefail
+
+        failures=()
+
+        # Where the current set of expected results lives in the cloud
+        expected_prefix="~{expected_output_prefix}"
+        # Remove a trailing slash if there is one
+        expected_prefix=${expected_prefix%/}
+
+        # Download all the expected data
+        mkdir expected
+        cd expected
+        # Make a FOFN for more efficient downloading
+        for file in ~{sep= ' ' actual_vcfs}; do
+            echo "$expected_prefix/$(basename $file)" >> expected_fofn.txt
+        done
+        # Download and unzip all the expected data
+        cat expected_fofn.txt | gsutil -m cp -I .
+        gzip -d *.gz
+        cd ..
+
+        # Also unzip actual result data
+        gzip -d ~{sep= ' ' actual_vcfs}
+
+        # Headers first, these can yield useful diagnostics when there are mismatches.
+        for file in ~{sep=' ' actual_vcfs}; do
+          unzipped=${file%.gz}
+          expected="expected/$(basename $unzipped)"
+          set +o errexit
+          cmp <(grep '^#' $unzipped) <(grep '^#' $expected)
+          rc=$?
+          set -o errexit
+          if [[ $rc -ne 0 ]]; then
+            # If there is a mismatch add it to a list of failures but keep on looking for mismatches.
+            failures+=( $unzipped )
+          fi
+        done
+
+        if [[ ${#failures[@]} -ne 0 ]]; then
+          echo "Error: headers for the following files do not match:"
+          for failure in ${failures[@]}; do
+            echo $(basename $failure)
+            expected="expected/$(basename $failure)"
+            diff $failure $expected
+          done
+          exit 1
+        fi
+
+        # If the headers all matched look for any mismatches in overall file content.
+        fail=0
+        for file in ~{sep=' ' actual_vcfs}; do
+          unzipped=${file%.gz}
+          expected="expected/$(basename $unzipped)"
+          set +o errexit
+          cmp $unzipped $expected
+          rc=$?
+          set -o errexit
+          if [[ $rc -ne 0 ]]; then
+            echo "Error: file contents of expected and actual do not match: $(basename $unzipped)"
+            fail=1
+          fi
+        done
+
+        if [[ $fail -ne 0 ]]; then
+          exit 1
+        fi
+
+        echo "All vcfs compared and matched!"
+    >>>
+
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
+        disks: "local-disk 500 HDD"
+    }
+
+    output {
+        File fofn = "expected/expected_fofn.txt"
+        Boolean done = true
+    }
+}
+
+task AssertCostIsTrackedAndExpected {
+    meta {
+        # we want to check the database each time this runs
+        volatile: true
+    }
+
+    input {
+        Boolean go = true
+        String dataset_name
+        String project_id
+        File expected_output_csv
+    }
+
+    command <<<
+        set -o errexit
+        set -o nounset
+        set -o pipefail
+
+        echo "project_id = ~{project_id}" > ~/.bigqueryrc
+        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
+            "SELECT call, step, event_key, sum(event_bytes) \
+              FROM \`~{dataset_name}.cost_observability\` \
+              GROUP BY call, step, event_key \
+              ORDER BY call, step, event_key" > cost_observability_output.csv
+
+        # Put the exit code in a file because we are using a subshell (while) later and changes to the variable *in* the subshell are lost
+        echo "0" > ret_val.txt
+
+        paste cost_observability_output.csv ~{expected_output_csv} | while  IFS=$'\t' read observed expected; do
+        IFS=, read -ra OBS <<< "$observed"
+        IFS=, read -ra EXP <<< "$expected"
+        if [[ "${#OBS[@]}" -ne 4  || "${#EXP[@]}" -ne 4 ]]; then
+          echo "Unexpected number of rows found in the input files"
+          exit 1
+        fi
+
+        OBS_KEY=${OBS[0]}.${OBS[1]}.${OBS[2]}
+        EXP_KEY=${EXP[0]}.${EXP[1]}.${EXP[2]}
+        if [[ "$OBS_KEY" != "$EXP_KEY" ]]; then
+          echo "Mismatched keys in results files - were these sorted properly?"
+          exit 1
+        fi
+
+        if [[ "$OBS_KEY" == "call.step.event_key" ]]; then
+          # Skip the header
+          continue;
+        fi
+
+        OBS_BYTES=${OBS[3]}
+        EXP_BYTES=${EXP[3]}
+
+        TOLERANCE=0
+
+        # For these two costs, there is non-determinism in the pipeline - we allow a % difference
+        if [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.BigQuery Query Scanned" ]]; then
+          TOLERANCE=0.015   # 1.5% tolerance  (Note - have seen as high as: 0.0109429)
+        elif [[ $OBS_KEY == "ExtractTask.GvsCreateCallset.Storage API Scanned" ]]; then
+          TOLERANCE=0.01   # 1% tolerance  (Note - have seen as high as: 0.00608656)
+        elif [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.Storage API Scanned" ]]; then
+          TOLERANCE=0.05  # 5% tolerance (Note - have seen as high as: 0.0281223)
+        fi
+
+        if [[ $OBS_BYTES -ne $EXP_BYTES ]]; then
+          echo "The bytes observed ($OBS_BYTES) for '$OBS_KEY' differ from those expected ($EXP_BYTES)"
+
+          if [[ $OBS_BYTES -ge $EXP_BYTES ]]; then
+            DIFF_FOUND=$(echo $OBS_BYTES $EXP_BYTES | awk '{print ($1-$2)/$1}')
+          else
+            DIFF_FOUND=$(echo $EXP_BYTES $OBS_BYTES | awk '{print ($1-$2)/$1}')
+          fi
+
+          if ! awk "BEGIN{ exit ($DIFF_FOUND > $TOLERANCE) }"
+          then
+            echo "FAIL!!! The relative difference between these is $DIFF_FOUND, which is greater than the allowed tolerance ($TOLERANCE)"
+            echo "1" > ret_val.txt
+          else
+            echo "However, the relative difference between these is $DIFF_FOUND, which is below the allowed tolerance ($TOLERANCE)"
+          fi
+        fi
+        done
+
+        RET_VAL=`cat ret_val.txt`
+        exit $RET_VAL
+
+    >>>
+
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
+        disks: "local-disk 10 HDD"
+    }
+
+    output {
+        File cost_observability_output_csv = "cost_observability_output.csv"
+    }
+}
+
+task AssertTableSizesAreExpected {
+    meta {
+        # we want to check the database each time this runs
+        volatile: true
+    }
+
+    input {
+        Boolean go = true
+        String dataset_name
+        String project_id
+        File expected_output_csv
+    }
+
+    command <<<
+        set -o errexit
+        set -o nounset
+        set -o pipefail
+
+        echo "project_id = ~{project_id}" > ~/.bigqueryrc
+        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
+            "SELECT 'vet_total' AS total_name, sum(total_billable_bytes) AS total_bytes FROM \
+            \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` WHERE table_name LIKE 'vet_%' \
+            UNION ALL \
+            SELECT 'ref_ranges_total' AS total_name, sum(total_billable_bytes) AS total_bytes \
+            FROM \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` \
+            WHERE table_name LIKE 'ref_ranges_%' ORDER BY total_name" > table_size_output.csv
+
+        set +o errexit
+        diff -w table_size_output.csv ~{expected_output_csv} > differences.txt
+        set -o errexit
+
+        if [[ -s differences.txt ]]; then
+            echo "Differences found:"
+            cat differences.txt
+            exit 1
+        fi
+    >>>
+
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
+        disks: "local-disk 10 HDD"
+    }
+
+    output {
+        File table_size_output_csv = "table_size_output.csv"
+        File differences = "differences.txt"
+    }
+}
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 5bac773b82c..d5799fa1804 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -117,6 +117,7 @@ workflow GvsUnifiedHail {
 
     output {
         Boolean done = true
+        String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
     }
 }
 

From 757fa2248cdf4d3c1ac3045e5eae128e9b62ca06 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 06:55:38 -0400
Subject: [PATCH 03/49] hopefully fail in more interesting ways

---
 scripts/monitoring_script.sh                | 290 ++++++++++++++++++++
 scripts/variantstore/wdl/GvsUnifiedHail.wdl |  12 +-
 2 files changed, 301 insertions(+), 1 deletion(-)
 create mode 100644 scripts/monitoring_script.sh

diff --git a/scripts/monitoring_script.sh b/scripts/monitoring_script.sh
new file mode 100644
index 00000000000..e5c313c300f
--- /dev/null
+++ b/scripts/monitoring_script.sh
@@ -0,0 +1,290 @@
+#!/bin/bash
+# NOTE: this script is intended to be placed in google cloud storage
+# and invoked by adding the following line to your cromwell workflow
+# options:
+#    "monitoring_script": "gs://bucket/path/to/cromwell_monitoring_script.sh"
+# Upon task completion "monitoring.log" will be added to the appropriate
+# cloud storage folder.
+set -Eeuo pipefail
+
+MONITOR_MOUNT_POINT=${MONITOR_MOUNT_POINT:-"/cromwell_root"}
+SLEEP_TIME=${SLEEP_TIME:-"10"}
+
+function getCpuUsage() {
+    # get the summary cpu statistics (i.e. for all cpus) since boot
+    # get the numeric values in an array, dropping the first field (the
+    # string, "cpu")
+    CPU_TIMES=(`sed -n 's/^cpu\s//p' /proc/stat`)
+    # idle time (in system units) is the 3rd numeric field
+    IDLE_TIME=${CPU_TIMES[3]}
+    # total cpu time is sum of all fields
+    TOTAL_TIME=0
+    for T in ${CPU_TIMES[@]}; do
+        ((TOTAL_TIME += T))
+    done
+
+    # get the previous times from temp file
+    read PREVIOUS_IDLE PREVIOUS_TOTAL < $TEMP_CPU
+
+    # write current times to temp file
+    echo "$IDLE_TIME $TOTAL_TIME" > $TEMP_CPU
+
+    # get the difference in idle and total times since the previous
+    # update, and report the usage as: non-idle time as a percentage
+    # of total time
+    awk -v IDLE=$((IDLE_TIME-PREVIOUS_IDLE)) \
+        -v TOTAL=$((TOTAL_TIME-PREVIOUS_TOTAL)) \
+        'BEGIN { printf "%.1f%%", 100 * (1 - IDLE / TOTAL) }'
+}
+
+function getMem() {
+    # get desired memory value from /proc/meminfo, in GiB, and also
+    # as a percentage of total
+    # argument is the label of the desired memory value
+    cat /proc/meminfo \
+        | awk -v MEM_FIELD="$1" '{
+            f[substr($1, 1, length($1)-1)] = $2
+        } END {
+            printf "%.2f GiB", f[MEM_FIELD] / 1048576
+        }'
+}
+
+function getMemUnavailable() {
+    # get unavailable memory from /proc/meminfo, in GiB
+    cat /proc/meminfo \
+        | awk '{
+            f[substr($1, 1, length($1)-1)] = $2
+        } END {
+
+            if("MemAvailable" in f) {
+                mem_available = f["MemAvailable"]
+            } else {
+                mem_available = f["MemFree"] + f["Buffers"] + f["Cached"]
+            }
+            mem_in_use = f["MemTotal"] - mem_available
+            printf "%.2f GiB %.1f%%", mem_in_use / 1048576, 100 * mem_in_use / f["MemTotal"]
+        }'
+}
+
+# old version using "free -m" are kept in case a container somehow has
+# weird values in /proc/meminfo
+function getMem_with_free() {
+    # get memory info from "free" command. Convert to float in GB.
+    # First argument is desired row of output table.
+    # Second argument is desired column.
+    MEM_ROW=$(echo "$1" | awk '{print tolower($1)}')
+    MEM_COLUMN=$(echo "$2" | awk '{print tolower($1)}')
+    free -m | awk -v MEM_ROW=$MEM_ROW -v MEM_COLUMN=$MEM_COLUMN \
+        'NR=1 {
+            for(i=1; i<=NF; i++) { f[tolower($i)]=NF+1-i }
+        }
+        {
+            regex="^"MEM_ROW
+            if(tolower($1) ~ regex) {
+                print $(NF+1-f[MEM_COLUMN])/1024 " GiB"
+            }
+        }'
+}
+
+# old version using "free -m" are kept in case a container somehow has
+# weird values in /proc/meminfo
+function getMemUnavailable_using_free() {
+    # get memory that is in active use (not just cached) from "free"
+    # command. Convert to float in GiB, followed by percent of total.
+    # NOTE: weird computation with awk due to variety of output from
+    # free on different systems. Rows and columns differ, and on some
+    # systems the desired quantity is used "used" memory, on most it's
+    # "used" - "buffers" - "cached". If "buffers" and "cached" don't
+    # exist, then awk will subtract 0 so the correct result is returned.
+    free -m \
+        | awk '\
+            NR=1 {
+                for(i=1; i<=NF; i++) { f[tolower($i)]=NF+1-i }
+            }
+            {
+                if(tolower($1) ~ "^mem") {
+                    IN_USE=($(NF+1-f["used"]) - $(NF+1-f["buffers"]) - $(NF+1-f["cached"]))
+                    printf "%.3f GiB %.1f%%", IN_USE/1024, 100*IN_USE/$(NF+1-f["total"])
+                }
+            }'
+}
+
+
+function getDisk() {
+    # get information about disk usage from "df" command.
+    DISK_COLUMN=$(echo "$1" | awk '{print tolower($1)}')
+    MOUNT_POINT=$2
+    # extract desired value
+    VALUE=$(\
+        df -h "$MOUNT_POINT" \
+        | sed 's/Mounted on/Mounted-on/' \
+        | awk -v DISK_COLUMN=$DISK_COLUMN '
+            FNR==1 {
+                NF_HEADER=NF
+                for(i=1; i<=NF; i++) { f[tolower($i)]=NF-i }
+            }
+            FNR>1 {
+                FIELD_NUM=NF-f[DISK_COLUMN]
+                if(FIELD_NUM > 0) {
+                    VALUE=$(FIELD_NUM)
+                    print VALUE
+                } else if(f[DISK_COLUMN] == NF_HEADER-1 && NF == 1) {
+                    VALUE=$(1)
+                    print VALUE
+                }
+            }' \
+    )
+    # If value is a number follwed by letters, it is a value with units
+    # and needs to be converted. Otherwise just print value
+    if [[ "$VALUE" =~ [0-9.]+[A-z]+ ]]; then
+        echo "$VALUE"\
+        | sed -E 's/([0-9.]*)([^0-9.]*)/\1 \2/' \
+        | awk '{
+            UNIT=substr($2, 1, 1)
+            if(UNIT == "T") {
+                SCALE=2^10
+            } else if(UNIT == "G") {
+                SCALE=1
+            } else if(UNIT == "M") {
+                SCALE=2^-10
+            } else if(UNIT == "K") {
+                SCALE=2^-20
+            } else if(UNIT == "B") {
+                SCALE=2^-30
+            } else {
+                SCALE=1
+            }
+            printf "%.3f GiB", $1 * SCALE
+        }'
+    else
+        echo "$VALUE"
+    fi
+}
+
+function findBlockDevice() {
+    MOUNT_POINT=$1
+    FILESYSTEM=$(grep -E "$MOUNT_POINT\s" /proc/self/mounts \
+                | awk '{print $1}')
+    DEVICE_NAME=$(basename "$FILESYSTEM")
+    FS_IN_BLOCK=$(find -L /sys/block/ -mindepth 2 -maxdepth 2 -type d \
+                       -name "$DEVICE_NAME")
+    if [ -n "$FS_IN_BLOCK" ]; then
+        # found path to the filesystem in the block devices. get the
+        # block device as the parent dir
+        dirname "$FS_IN_BLOCK"
+    elif [ -d "/sys/block/$DEVICE_NAME" ]; then
+        # the device is itself a block device
+        echo "/sys/block/$DEVICE_NAME"
+    else
+        # couldn't find, possibly mounted by mapper.
+        # look for block device that is just the name of the symlinked
+        # original file. if not found, echo empty string (no device found)
+        BLOCK_DEVICE=$(ls -l "$FILESYSTEM" 2>/dev/null \
+                        | cut -d'>' -f2 \
+                        | xargs basename 2>/dev/null \
+                        || echo)
+        if [[ -z "$BLOCK_DEVICE" ]]; then
+            1>&2 echo "Unable to find block device for filesystem $FILESYSTEM."
+            if [[ -d /sys/block/sdb ]] && ! grep -qE "^/dev/sdb" /etc/mtab; then
+                1>&2 echo "Guessing present but unused sdb is the correct block device."
+                echo "/sys/block/sdb"
+            else
+                1>&2 echo "Disk IO will not be monitored."
+            fi
+        fi
+    fi
+}
+
+function handle_integer_wrap() {
+    if [ $1 -ge 0 ]; then
+        echo $1
+    else
+        WRAPPED=$1
+        echo "$((WRAPPED + 2**30))"
+    fi
+}
+
+
+
+function getBlockDeviceIO() {
+    # get read and write IO rate by looking at appropriate block device
+    STAT_FILE="$1"
+    if [[ -f "$STAT_FILE" ]]; then
+        # get IO stats as comma-separated list to extract 3rd and 7th fields
+        STATS=$(sed -E 's/[[:space:]]+/,/g' $STAT_FILE | sed -E 's/^,//'\
+                | cut -d, -f3,7 | sed -E 's/,/ /g')
+        # get results of previous poll
+        read OLD_READ OLD_WRITE < $TEMP_IO
+        # save new poll results
+        read READ_SECTORS WRITE_SECTORS <<<$STATS
+        echo "$READ_SECTORS $WRITE_SECTORS" > $TEMP_IO
+        # update read and write sectors as difference since previous poll
+        READ_SECTORS=$(handle_integer_wrap $((READ_SECTORS - OLD_READ)))
+        WRITE_SECTORS=$(handle_integer_wrap $((WRITE_SECTORS - OLD_WRITE)))
+
+        # output change in read/write sectors in kiB/s
+        echo "$READ_SECTORS $WRITE_SECTORS" \
+            | awk -v T=$SLEEP_TIME -v B=$SECTOR_BYTES \
+                '{ printf "%.3f MiB/s %.3f MiB/s",  $1*B/T/1048576, $2*B/T/1048576 }'
+    else
+        echo "N/A MiB/s N/A MiB/s"
+    fi
+}
+
+
+function runtimeInfo() {
+    echo [$(date)]
+    echo \* CPU usage: $(getCpuUsage)
+    echo \* Memory usage: $(getMemUnavailable)
+    echo \* Disk usage: $(getDisk Used $MONITOR_MOUNT_POINT) $(getDisk Use% $MONITOR_MOUNT_POINT)
+    echo \* Read/Write IO: $(getBlockDeviceIO "$BLOCK_DEVICE_STAT_FILE")
+}
+
+# print out header info
+echo ==================================
+echo =========== MONITORING ===========
+echo ==================================
+echo --- General Information ---
+echo \#CPU: $(nproc)
+echo Total Memory: $(getMem MemTotal)
+echo Total Disk space: $(getDisk Size "$MONITOR_MOUNT_POINT")
+echo
+echo --- Runtime Information ---
+
+
+# make a temp file to store io information, remove it on exit
+TEMP_IO=$(mktemp "${TMPDIR:-/tmp/}$(basename $0).XXXXXXXXXXXX")
+# make a temp file to store cpu information, remove it on exit
+# remove temp files on exit
+TEMP_CPU=$(mktemp "${TMPDIR:-/tmp/}$(basename $0).XXXXXXXXXXXX")
+trap "rm -f $TEMP_IO $TEMP_CPU" EXIT
+
+
+# find the block device
+BLOCK_DEVICE=$(findBlockDevice "$MONITOR_MOUNT_POINT")
+if [[ -z "$BLOCK_DEVICE" ]] \
+        || [[ ! -f "$BLOCK_DEVICE/queue/hw_sector_size" ]]; then
+    # no block device found, can't get IO info
+    SECTOR_BYTES=0
+    BLOCK_DEVICE_STAT_FILE=""
+else
+    SECTOR_BYTES=$(cat "$BLOCK_DEVICE/queue/hw_sector_size")
+    BLOCK_DEVICE_STAT_FILE="$BLOCK_DEVICE/stat"
+fi
+
+
+# since getBlockDeviceIO looks at differences in stat file, run the
+# update so the first reported update has a sensible previous result to
+# compare to
+echo "0 0" > $TEMP_IO
+getBlockDeviceIO "$BLOCK_DEVICE_STAT_FILE" > /dev/null
+
+# same thing for getCpuUsage
+echo "0 0" > $TEMP_CPU
+getCpuUsage > /dev/null
+
+
+while true; do
+    runtimeInfo
+    sleep $SLEEP_TIME
+done
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index d5799fa1804..c4d6703376f 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -131,13 +131,23 @@ task CreateVds {
         PS4='\D{+%F %T} \w $ '
         set -o errexit -o nounset -o pipefail -o xtrace
 
+        # Temurin Java 8
+        apt-get -qq install wget apt-transport-https gnupg
+        wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | apt-key add -
+        echo "deb https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
+        apt-get -qq update
+        apt -qq install -y temurin-8-jdk
+
+        export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
+        curl --silent --show-error --location https://broad.io/install-gcs-connector | python3
+
         pip install ~{hail_wheel}
         python3 ~{hail_gvs_import_script}
     >>>
     runtime {
         docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-24-alpine"
         disks: "local-disk 500 HDD"
-        cpu: 8
+        memory: "30 GiB"
     }
     output {
         Boolean done = true

From 059e7b1d6ad8087f886d7dd610c19f66b2c73c3d Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 11:29:43 -0400
Subject: [PATCH 04/49] spike-worthy hackery

---
 .../wdl/GvsQuickstartHailIntegration.wdl      |   2 +-
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   | 121 +++++++++---------
 2 files changed, 62 insertions(+), 61 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 9140384dea7..475ab506aea 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -94,7 +94,7 @@ workflow GvsQuickstartHailIntegration {
 #    }
 #
     output {
-        String vds_output_path = GvsUnifiedHail.vds_output_path
+        # String vds_output_path = GvsUnifiedHail.vds_output_path
         Boolean done = true
     }
 }
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index c4d6703376f..0f710066c08 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -51,73 +51,74 @@ workflow GvsUnifiedHail {
         # End CreateVds
     }
 
-    call AssignIds.GvsAssignIds as AssignIds {
-        input:
-            dataset_name = dataset_name,
-            project_id = project_id,
-            external_sample_names = external_sample_names,
-            assign_ids_gatk_override = gatk_override
-    }
-
-    call ImportGenomes.GvsImportGenomes {
-        input:
-            go = AssignIds.done,
-            dataset_name = dataset_name,
-            project_id = project_id,
-            external_sample_names = external_sample_names,
-            input_vcfs = input_vcfs,
-            input_vcf_indexes = input_vcf_indexes,
-            interval_list = interval_list,
-            load_data_preemptible_override = load_data_preemptible_override,
-            load_data_maxretries_override = load_data_maxretries_override,
-            load_data_gatk_override = gatk_override,
-            load_data_batch_size = load_data_batch_size,
-            drop_state = drop_state
-    }
-
-    call PopulateAltAllele.GvsPopulateAltAllele {
-        input:
-            call_set_identifier = call_set_identifier,
-            go = GvsImportGenomes.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,
-            indel_recalibration_annotation_values = indel_recalibration_annotation_values,
-            snp_recalibration_annotation_values = snp_recalibration_annotation_values,
-            interval_list = interval_list,
-            gatk_override = gatk_override,
-            INDEL_VQSR_max_gaussians_override = INDEL_VQSR_max_gaussians_override,
-            INDEL_VQSR_mem_gb_override = INDEL_VQSR_mem_gb_override,
-            SNP_VQSR_max_gaussians_override = SNP_VQSR_max_gaussians_override,
-            SNP_VQSR_mem_gb_override = SNP_VQSR_mem_gb_override
-    }
-
-    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
-        input:
-            go = GvsCreateFilterSet.done,
-            project_id = project_id,
-            dataset = dataset_name,
-            filter_set_name = filter_set_name,
-            scatter_width = 10,
-    }
+#    call AssignIds.GvsAssignIds as AssignIds {
+#        input:
+#            dataset_name = dataset_name,
+#            project_id = project_id,
+#            external_sample_names = external_sample_names,
+#            assign_ids_gatk_override = gatk_override
+#    }
+#
+#    call ImportGenomes.GvsImportGenomes {
+#        input:
+#            go = AssignIds.done,
+#            dataset_name = dataset_name,
+#            project_id = project_id,
+#            external_sample_names = external_sample_names,
+#            input_vcfs = input_vcfs,
+#            input_vcf_indexes = input_vcf_indexes,
+#            interval_list = interval_list,
+#            load_data_preemptible_override = load_data_preemptible_override,
+#            load_data_maxretries_override = load_data_maxretries_override,
+#            load_data_gatk_override = gatk_override,
+#            load_data_batch_size = load_data_batch_size,
+#            drop_state = drop_state
+#    }
+#
+#    call PopulateAltAllele.GvsPopulateAltAllele {
+#        input:
+#            call_set_identifier = call_set_identifier,
+#            go = GvsImportGenomes.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,
+#            indel_recalibration_annotation_values = indel_recalibration_annotation_values,
+#            snp_recalibration_annotation_values = snp_recalibration_annotation_values,
+#            interval_list = interval_list,
+#            gatk_override = gatk_override,
+#            INDEL_VQSR_max_gaussians_override = INDEL_VQSR_max_gaussians_override,
+#            INDEL_VQSR_mem_gb_override = INDEL_VQSR_mem_gb_override,
+#            SNP_VQSR_max_gaussians_override = SNP_VQSR_max_gaussians_override,
+#            SNP_VQSR_mem_gb_override = SNP_VQSR_mem_gb_override
+#    }
+#
+#    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
+#        input:
+#            go = GvsCreateFilterSet.done,
+#            project_id = project_id,
+#            dataset = dataset_name,
+#            filter_set_name = filter_set_name,
+#            scatter_width = 10,
+#    }
 
     call CreateVds {
         input:
-            hail_gvs_import_script = GvsExtractAvroFilesForHail.hail_gvs_import_script,
+            # hail_gvs_import_script = GvsExtractAvroFilesForHail.hail_gvs_import_script,
+            hail_gvs_import_script = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-GenerateHailScripts/hail_gvs_import.py",
             hail_wheel = hail_wheel,
     }
 
     output {
         Boolean done = true
-        String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
+        # String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
     }
 }
 
@@ -138,10 +139,10 @@ task CreateVds {
         apt-get -qq update
         apt -qq install -y temurin-8-jdk
 
+        pip install ~{hail_wheel}
         export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
         curl --silent --show-error --location https://broad.io/install-gcs-connector | python3
 
-        pip install ~{hail_wheel}
         python3 ~{hail_gvs_import_script}
     >>>
     runtime {

From c422cf8c0fb177c10421adad4b366b1742852aef Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 11:51:09 -0400
Subject: [PATCH 05/49] increase hackery

---
 .../wdl/GvsQuickstartHailIntegration.wdl            | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 475ab506aea..dc288005728 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -52,19 +52,18 @@ workflow GvsQuickstartHailIntegration {
     }
     String project_id = "gvs-internal"
 
-    call Utils.BuildGATKJarAndCreateDataset {
-        input:
-            branch_name = branch_name,
-            dataset_prefix = "quickit"
-    }
+#    call Utils.BuildGATKJarAndCreateDataset {
+#        input:
+#            branch_name = branch_name,
+#            dataset_prefix = "quickit"
+#    }
 
     call Unified.GvsUnifiedHail {
         input:
             call_set_identifier = branch_name,
-            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+            dataset_name = "quickit_vs_639_hail_testing_spike_80af46a",
             project_id = project_id,
             external_sample_names = external_sample_names,
-            gatk_override = BuildGATKJarAndCreateDataset.jar,
             input_vcfs = input_vcfs,
             input_vcf_indexes = input_vcf_indexes,
             filter_set_name = "quickit",

From 7a1ea9066b2a41316393ff109ee349fdbf795e3a Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 12:09:17 -0400
Subject: [PATCH 06/49] huh

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 0f710066c08..ff7f7002de7 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -146,7 +146,7 @@ task CreateVds {
         python3 ~{hail_gvs_import_script}
     >>>
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-24-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-slim"
         disks: "local-disk 500 HDD"
         memory: "30 GiB"
     }

From f41226ed253d6d77ff5625afb5d0ecda86cbda46 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 12:23:14 -0400
Subject: [PATCH 07/49] maybe

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index ff7f7002de7..9e81e2b787b 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -141,6 +141,7 @@ task CreateVds {
 
         pip install ~{hail_wheel}
         export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
+        gcloud auth application-default login
         curl --silent --show-error --location https://broad.io/install-gcs-connector | python3
 
         python3 ~{hail_gvs_import_script}

From c62a283e4bec4c49eecf953779b7758c69f265ca Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 18:35:45 -0400
Subject: [PATCH 08/49] wip

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   |  9 +-
 .../wdl/extract/hail_gvs_import.py            | 95 +++++++++++++++----
 .../wdl/extract/test_hail_gvs_import.py       |  6 +-
 3 files changed, 84 insertions(+), 26 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 9e81e2b787b..5d5f264ece8 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -132,6 +132,8 @@ task CreateVds {
         PS4='\D{+%F %T} \w $ '
         set -o errexit -o nounset -o pipefail -o xtrace
 
+        gcloud storage --recursive ~{avro_prefix}
+
         # Temurin Java 8
         apt-get -qq install wget apt-transport-https gnupg
         wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | apt-key add -
@@ -141,14 +143,13 @@ task CreateVds {
 
         pip install ~{hail_wheel}
         export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
-        gcloud auth application-default login
-        curl --silent --show-error --location https://broad.io/install-gcs-connector | python3
 
-        python3 ~{hail_gvs_import_script}
+        export
+        python3 ~{hail_gvs_import_script} --
     >>>
     runtime {
         docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-slim"
-        disks: "local-disk 500 HDD"
+        disks: "local-disk 2000 HDD"
         memory: "30 GiB"
     }
     output {
diff --git a/scripts/variantstore/wdl/extract/hail_gvs_import.py b/scripts/variantstore/wdl/extract/hail_gvs_import.py
index 8c395954422..ade735dacc0 100644
--- a/scripts/variantstore/wdl/extract/hail_gvs_import.py
+++ b/scripts/variantstore/wdl/extract/hail_gvs_import.py
@@ -32,10 +32,11 @@
 from google.cloud import storage
 
 import argparse
+import os
 import re
 
 
-def generate_avro_args(bucket, blob_prefix, key):
+def generate_gcs_avro_args(bucket, blob_prefix, key):
     """
     Generate a list of the Avro arguments for the `hl.import_gvs` invocation for the specified key. The datatype should
     match the parameters of the `hl.import_gvs` function:
@@ -83,7 +84,7 @@ def regular_handler(blob_name):
     return ret
 
 
-def import_gvs(bucket, object_prefix, vds_output_path, tmp_dir):
+def import_gvs_gcs(bucket, object_prefix, vds_output_path, tmp_dir):
     import hail as hl
 
     unslashed_tmp_dir = tmp_dir if not tmp_dir.endswith('/') else tmp_dir[:-1]
@@ -94,7 +95,58 @@ def import_gvs(bucket, object_prefix, vds_output_path, tmp_dir):
                       'gs://hail-common/references/Homo_sapiens_assembly38.fasta.fai')
 
     def args(key):
-        return generate_avro_args(bucket, object_prefix, key)
+        return generate_gcs_avro_args(bucket, object_prefix, key)
+
+    hl.import_gvs(
+        vets=args('vets'),
+        refs=args('refs'),
+        sample_mapping=args('sample_mapping'),
+        site_filtering_data=args('site_filtering_data'),
+        vqsr_filtering_data=args('vqsr_filtering_data'),
+        vqsr_tranche_data=args('vqsr_tranche_data'),
+        reference_genome=rg38,
+        final_path=vds_output_path,
+        tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_import_gvs'
+    )
+
+
+def generate_local_avro_args(avro_prefix, key):
+    def superpartitioned_handler():
+        parts = root.split('/')
+
+        index = int(parts[-1].split('_')[-1]) - 1
+        if len(ret) == index:
+            ret.append([])
+        ret[index].append(f'{root}/{file}')
+
+    def regular_handler():
+        ret.append(f'{root}/{file}')
+
+    superpartitioned_keys = {'vets', 'refs'}
+    entry_handler = superpartitioned_handler if key in superpartitioned_keys else regular_handler
+
+    ret = []
+
+    for root, dir, files in os.walk(f'{avro_prefix}/{key}'):
+        for file in files:
+            if file.endswith('avro'):
+                entry_handler()
+    return ret
+
+
+def import_gvs_local(avro_prefix, tmp_dir, vds_output_path, references_dir):
+    import hail as hl
+
+    unslashed_tmp_dir = tmp_dir if not tmp_dir.endswith('/') else tmp_dir[:-1]
+    hl.init(tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_general')
+
+    references_dir = references_dir[:-1] if references_dir.endswith('/') else references_dir
+    rg38 = hl.get_reference('GRCh38')
+    rg38.add_sequence(f'{references_dir}/Homo_sapiens_assembly38.fasta.gz',
+                      f'{references_dir}/Homo_sapiens_assembly38.fasta.fai')
+
+    def args(key):
+        return generate_local_avro_args(avro_prefix, key)
 
     hl.import_gvs(
         vets=args('vets'),
@@ -112,11 +164,13 @@ def args(key):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(allow_abbrev=False,
                                      description='Create base Hail VDS from exported GVS Avro files.')
-    parser.add_argument('--avro_prefix', type=str, help='GCS prefix under which exported GVS Avro files are found',
+    parser.add_argument('--avro_prefix', type=str, help='Prefix under which exported GVS Avro files are found',
                         default="@AVRO_PREFIX@")
     parser.add_argument('--write_prefix', type=str,
-                        help='GCS prefix to which VDS and temporary outputs should be written',
+                        help='Prefix to which VDS and temporary outputs should be written',
                         default="@WRITE_PREFIX@")
+    parser.add_argument('--references-dir', type=str,
+                        help='Path to references, only required for local files')
 
     args = parser.parse_args()
 
@@ -127,22 +181,25 @@ def args(key):
     avro_prefix = avro_prefix if not avro_prefix.endswith('/') else avro_prefix[:-1]
     write_prefix = write_prefix if not write_prefix.endswith('/') else write_prefix[:-1]
 
+    temp_dir = f"{write_prefix}/temp_hail_gvs_import"
+    vds_output_path = f"{write_prefix}/gvs_export.vds"
+
     gcs_re = re.compile("^gs://(?P<bucket_name>[^/]+)/(?P<object_prefix>.*)$")
     match = gcs_re.match(avro_prefix)
-    if not match:
-        raise ValueError(f"Avro prefix '{avro_prefix}' does not look like a GCS path")
-    avro_bucket_name, avro_object_prefix = match.groups()
+    if match:
+        avro_bucket_name, avro_object_prefix = match.groups()
+        match = gcs_re.match(avro_prefix)
+        if not match:
+            raise ValueError(f"Avro prefix '{write_prefix}' does not look like a GCS path")
+        client = storage.Client()
+        avro_bucket = client.get_bucket(avro_bucket_name)
+        import_gvs_gcs(avro_bucket, avro_object_prefix, vds_output_path, temp_dir)
+    else:
+        # assume local filesystem
+        references_dir = args.references_dir
+        if not references_dir:
+            raise ValueError(f"--references-dir must be specified with local files")
+        import_gvs_local(avro_prefix, temp_dir, vds_output_path, references_dir)
 
-    match = gcs_re.match(write_prefix)
-    if not match:
-        raise ValueError(f"Write prefix '{write_prefix}' does not look like a GCS path")
-
-    client = storage.Client()
-    avro_bucket = client.get_bucket(avro_bucket_name)
-
-    temp_dir = f"{write_prefix}/temp_hail_gvs_import"
-    vds_output_path = f"{write_prefix}/gvs_export.vds"
     print(f"Hail import temporary path: {temp_dir}")
     print(f"Final VDS location: {vds_output_path}.")
-
-    import_gvs(avro_bucket, avro_object_prefix, vds_output_path, temp_dir)
diff --git a/scripts/variantstore/wdl/extract/test_hail_gvs_import.py b/scripts/variantstore/wdl/extract/test_hail_gvs_import.py
index f6944e653d6..359df1101fb 100644
--- a/scripts/variantstore/wdl/extract/test_hail_gvs_import.py
+++ b/scripts/variantstore/wdl/extract/test_hail_gvs_import.py
@@ -1,6 +1,6 @@
 import unittest
 
-from hail_gvs_import import generate_avro_args
+from hail_gvs_import import generate_gcs_avro_args
 from unittest.mock import MagicMock
 
 
@@ -31,7 +31,7 @@ def test_generate_avro_arguments(self):
         bucket = ShamBucket(bucket_name)
         bucket.list_blobs = MagicMock(return_value=blobs)
 
-        actual = generate_avro_args(
+        actual = generate_gcs_avro_args(
             bucket=bucket,
             blob_prefix=blob_prefix,
             key='sample_mapping'
@@ -54,7 +54,7 @@ def test_generate_avro_arguments(self):
         ]
 
         bucket.list_blobs = MagicMock(return_value=blobs)
-        actual = generate_avro_args(
+        actual = generate_gcs_avro_args(
             bucket=bucket,
             blob_prefix=blob_prefix,
             key='vets'

From d835a2e2df04bdddd0ce60df27d43bb022b85f5c Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 19:02:11 -0400
Subject: [PATCH 09/49] wip

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl | 22 +++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 5d5f264ece8..7c765a9b417 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -111,9 +111,10 @@ workflow GvsUnifiedHail {
 
     call CreateVds {
         input:
-            # hail_gvs_import_script = GvsExtractAvroFilesForHail.hail_gvs_import_script,
             hail_gvs_import_script = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-GenerateHailScripts/hail_gvs_import.py",
             hail_wheel = hail_wheel,
+            avro_prefix = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/avro",
+            vds_destination_path = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/gvs_export.vds"
     }
 
     output {
@@ -126,13 +127,23 @@ task CreateVds {
     input {
         File hail_gvs_import_script
         File hail_wheel
+        String avro_prefix
+        String vds_destination_path
     }
     command <<<
         # Prepend date, time and pwd to xtrace log entries.
         PS4='\D{+%F %T} \w $ '
         set -o errexit -o nounset -o pipefail -o xtrace
 
-        gcloud storage --recursive ~{avro_prefix}
+        export AVRO=$PWD/avro
+        mkdir -p ${AVRO}
+
+        gsutil ls -r ~{avro_prefix} | grep -E '\.avro$' | gcloud storage cp -I ${AVRO}
+
+        export REFERENCES=$PWD/references
+        mkdir -p ${REFERENCES}
+
+        gcloud storage cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta*' ${REFERENCES}
 
         # Temurin Java 8
         apt-get -qq install wget apt-transport-https gnupg
@@ -144,8 +155,11 @@ task CreateVds {
         pip install ~{hail_wheel}
         export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
 
-        export
-        python3 ~{hail_gvs_import_script} --
+        export WORK=$PWD/work
+        mkdir ${WORK}
+        python3 ~{hail_gvs_import_script} --avro_prefix ${AVRO} --write_prefix ${WORK} --references-dir ${REFERENCES}
+
+        gcloud storage cp --recursive ${WORK}/gvs_export.vds ~{vds_destination_path}
     >>>
     runtime {
         docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-slim"

From bc3d001aab684720d6ff3e749405b3d4d94966fa Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 19:02:55 -0400
Subject: [PATCH 10/49] doh

---
 scripts/monitoring_script.sh | 290 -----------------------------------
 1 file changed, 290 deletions(-)
 delete mode 100644 scripts/monitoring_script.sh

diff --git a/scripts/monitoring_script.sh b/scripts/monitoring_script.sh
deleted file mode 100644
index e5c313c300f..00000000000
--- a/scripts/monitoring_script.sh
+++ /dev/null
@@ -1,290 +0,0 @@
-#!/bin/bash
-# NOTE: this script is intended to be placed in google cloud storage
-# and invoked by adding the following line to your cromwell workflow
-# options:
-#    "monitoring_script": "gs://bucket/path/to/cromwell_monitoring_script.sh"
-# Upon task completion "monitoring.log" will be added to the appropriate
-# cloud storage folder.
-set -Eeuo pipefail
-
-MONITOR_MOUNT_POINT=${MONITOR_MOUNT_POINT:-"/cromwell_root"}
-SLEEP_TIME=${SLEEP_TIME:-"10"}
-
-function getCpuUsage() {
-    # get the summary cpu statistics (i.e. for all cpus) since boot
-    # get the numeric values in an array, dropping the first field (the
-    # string, "cpu")
-    CPU_TIMES=(`sed -n 's/^cpu\s//p' /proc/stat`)
-    # idle time (in system units) is the 3rd numeric field
-    IDLE_TIME=${CPU_TIMES[3]}
-    # total cpu time is sum of all fields
-    TOTAL_TIME=0
-    for T in ${CPU_TIMES[@]}; do
-        ((TOTAL_TIME += T))
-    done
-
-    # get the previous times from temp file
-    read PREVIOUS_IDLE PREVIOUS_TOTAL < $TEMP_CPU
-
-    # write current times to temp file
-    echo "$IDLE_TIME $TOTAL_TIME" > $TEMP_CPU
-
-    # get the difference in idle and total times since the previous
-    # update, and report the usage as: non-idle time as a percentage
-    # of total time
-    awk -v IDLE=$((IDLE_TIME-PREVIOUS_IDLE)) \
-        -v TOTAL=$((TOTAL_TIME-PREVIOUS_TOTAL)) \
-        'BEGIN { printf "%.1f%%", 100 * (1 - IDLE / TOTAL) }'
-}
-
-function getMem() {
-    # get desired memory value from /proc/meminfo, in GiB, and also
-    # as a percentage of total
-    # argument is the label of the desired memory value
-    cat /proc/meminfo \
-        | awk -v MEM_FIELD="$1" '{
-            f[substr($1, 1, length($1)-1)] = $2
-        } END {
-            printf "%.2f GiB", f[MEM_FIELD] / 1048576
-        }'
-}
-
-function getMemUnavailable() {
-    # get unavailable memory from /proc/meminfo, in GiB
-    cat /proc/meminfo \
-        | awk '{
-            f[substr($1, 1, length($1)-1)] = $2
-        } END {
-
-            if("MemAvailable" in f) {
-                mem_available = f["MemAvailable"]
-            } else {
-                mem_available = f["MemFree"] + f["Buffers"] + f["Cached"]
-            }
-            mem_in_use = f["MemTotal"] - mem_available
-            printf "%.2f GiB %.1f%%", mem_in_use / 1048576, 100 * mem_in_use / f["MemTotal"]
-        }'
-}
-
-# old version using "free -m" are kept in case a container somehow has
-# weird values in /proc/meminfo
-function getMem_with_free() {
-    # get memory info from "free" command. Convert to float in GB.
-    # First argument is desired row of output table.
-    # Second argument is desired column.
-    MEM_ROW=$(echo "$1" | awk '{print tolower($1)}')
-    MEM_COLUMN=$(echo "$2" | awk '{print tolower($1)}')
-    free -m | awk -v MEM_ROW=$MEM_ROW -v MEM_COLUMN=$MEM_COLUMN \
-        'NR=1 {
-            for(i=1; i<=NF; i++) { f[tolower($i)]=NF+1-i }
-        }
-        {
-            regex="^"MEM_ROW
-            if(tolower($1) ~ regex) {
-                print $(NF+1-f[MEM_COLUMN])/1024 " GiB"
-            }
-        }'
-}
-
-# old version using "free -m" are kept in case a container somehow has
-# weird values in /proc/meminfo
-function getMemUnavailable_using_free() {
-    # get memory that is in active use (not just cached) from "free"
-    # command. Convert to float in GiB, followed by percent of total.
-    # NOTE: weird computation with awk due to variety of output from
-    # free on different systems. Rows and columns differ, and on some
-    # systems the desired quantity is used "used" memory, on most it's
-    # "used" - "buffers" - "cached". If "buffers" and "cached" don't
-    # exist, then awk will subtract 0 so the correct result is returned.
-    free -m \
-        | awk '\
-            NR=1 {
-                for(i=1; i<=NF; i++) { f[tolower($i)]=NF+1-i }
-            }
-            {
-                if(tolower($1) ~ "^mem") {
-                    IN_USE=($(NF+1-f["used"]) - $(NF+1-f["buffers"]) - $(NF+1-f["cached"]))
-                    printf "%.3f GiB %.1f%%", IN_USE/1024, 100*IN_USE/$(NF+1-f["total"])
-                }
-            }'
-}
-
-
-function getDisk() {
-    # get information about disk usage from "df" command.
-    DISK_COLUMN=$(echo "$1" | awk '{print tolower($1)}')
-    MOUNT_POINT=$2
-    # extract desired value
-    VALUE=$(\
-        df -h "$MOUNT_POINT" \
-        | sed 's/Mounted on/Mounted-on/' \
-        | awk -v DISK_COLUMN=$DISK_COLUMN '
-            FNR==1 {
-                NF_HEADER=NF
-                for(i=1; i<=NF; i++) { f[tolower($i)]=NF-i }
-            }
-            FNR>1 {
-                FIELD_NUM=NF-f[DISK_COLUMN]
-                if(FIELD_NUM > 0) {
-                    VALUE=$(FIELD_NUM)
-                    print VALUE
-                } else if(f[DISK_COLUMN] == NF_HEADER-1 && NF == 1) {
-                    VALUE=$(1)
-                    print VALUE
-                }
-            }' \
-    )
-    # If value is a number follwed by letters, it is a value with units
-    # and needs to be converted. Otherwise just print value
-    if [[ "$VALUE" =~ [0-9.]+[A-z]+ ]]; then
-        echo "$VALUE"\
-        | sed -E 's/([0-9.]*)([^0-9.]*)/\1 \2/' \
-        | awk '{
-            UNIT=substr($2, 1, 1)
-            if(UNIT == "T") {
-                SCALE=2^10
-            } else if(UNIT == "G") {
-                SCALE=1
-            } else if(UNIT == "M") {
-                SCALE=2^-10
-            } else if(UNIT == "K") {
-                SCALE=2^-20
-            } else if(UNIT == "B") {
-                SCALE=2^-30
-            } else {
-                SCALE=1
-            }
-            printf "%.3f GiB", $1 * SCALE
-        }'
-    else
-        echo "$VALUE"
-    fi
-}
-
-function findBlockDevice() {
-    MOUNT_POINT=$1
-    FILESYSTEM=$(grep -E "$MOUNT_POINT\s" /proc/self/mounts \
-                | awk '{print $1}')
-    DEVICE_NAME=$(basename "$FILESYSTEM")
-    FS_IN_BLOCK=$(find -L /sys/block/ -mindepth 2 -maxdepth 2 -type d \
-                       -name "$DEVICE_NAME")
-    if [ -n "$FS_IN_BLOCK" ]; then
-        # found path to the filesystem in the block devices. get the
-        # block device as the parent dir
-        dirname "$FS_IN_BLOCK"
-    elif [ -d "/sys/block/$DEVICE_NAME" ]; then
-        # the device is itself a block device
-        echo "/sys/block/$DEVICE_NAME"
-    else
-        # couldn't find, possibly mounted by mapper.
-        # look for block device that is just the name of the symlinked
-        # original file. if not found, echo empty string (no device found)
-        BLOCK_DEVICE=$(ls -l "$FILESYSTEM" 2>/dev/null \
-                        | cut -d'>' -f2 \
-                        | xargs basename 2>/dev/null \
-                        || echo)
-        if [[ -z "$BLOCK_DEVICE" ]]; then
-            1>&2 echo "Unable to find block device for filesystem $FILESYSTEM."
-            if [[ -d /sys/block/sdb ]] && ! grep -qE "^/dev/sdb" /etc/mtab; then
-                1>&2 echo "Guessing present but unused sdb is the correct block device."
-                echo "/sys/block/sdb"
-            else
-                1>&2 echo "Disk IO will not be monitored."
-            fi
-        fi
-    fi
-}
-
-function handle_integer_wrap() {
-    if [ $1 -ge 0 ]; then
-        echo $1
-    else
-        WRAPPED=$1
-        echo "$((WRAPPED + 2**30))"
-    fi
-}
-
-
-
-function getBlockDeviceIO() {
-    # get read and write IO rate by looking at appropriate block device
-    STAT_FILE="$1"
-    if [[ -f "$STAT_FILE" ]]; then
-        # get IO stats as comma-separated list to extract 3rd and 7th fields
-        STATS=$(sed -E 's/[[:space:]]+/,/g' $STAT_FILE | sed -E 's/^,//'\
-                | cut -d, -f3,7 | sed -E 's/,/ /g')
-        # get results of previous poll
-        read OLD_READ OLD_WRITE < $TEMP_IO
-        # save new poll results
-        read READ_SECTORS WRITE_SECTORS <<<$STATS
-        echo "$READ_SECTORS $WRITE_SECTORS" > $TEMP_IO
-        # update read and write sectors as difference since previous poll
-        READ_SECTORS=$(handle_integer_wrap $((READ_SECTORS - OLD_READ)))
-        WRITE_SECTORS=$(handle_integer_wrap $((WRITE_SECTORS - OLD_WRITE)))
-
-        # output change in read/write sectors in kiB/s
-        echo "$READ_SECTORS $WRITE_SECTORS" \
-            | awk -v T=$SLEEP_TIME -v B=$SECTOR_BYTES \
-                '{ printf "%.3f MiB/s %.3f MiB/s",  $1*B/T/1048576, $2*B/T/1048576 }'
-    else
-        echo "N/A MiB/s N/A MiB/s"
-    fi
-}
-
-
-function runtimeInfo() {
-    echo [$(date)]
-    echo \* CPU usage: $(getCpuUsage)
-    echo \* Memory usage: $(getMemUnavailable)
-    echo \* Disk usage: $(getDisk Used $MONITOR_MOUNT_POINT) $(getDisk Use% $MONITOR_MOUNT_POINT)
-    echo \* Read/Write IO: $(getBlockDeviceIO "$BLOCK_DEVICE_STAT_FILE")
-}
-
-# print out header info
-echo ==================================
-echo =========== MONITORING ===========
-echo ==================================
-echo --- General Information ---
-echo \#CPU: $(nproc)
-echo Total Memory: $(getMem MemTotal)
-echo Total Disk space: $(getDisk Size "$MONITOR_MOUNT_POINT")
-echo
-echo --- Runtime Information ---
-
-
-# make a temp file to store io information, remove it on exit
-TEMP_IO=$(mktemp "${TMPDIR:-/tmp/}$(basename $0).XXXXXXXXXXXX")
-# make a temp file to store cpu information, remove it on exit
-# remove temp files on exit
-TEMP_CPU=$(mktemp "${TMPDIR:-/tmp/}$(basename $0).XXXXXXXXXXXX")
-trap "rm -f $TEMP_IO $TEMP_CPU" EXIT
-
-
-# find the block device
-BLOCK_DEVICE=$(findBlockDevice "$MONITOR_MOUNT_POINT")
-if [[ -z "$BLOCK_DEVICE" ]] \
-        || [[ ! -f "$BLOCK_DEVICE/queue/hw_sector_size" ]]; then
-    # no block device found, can't get IO info
-    SECTOR_BYTES=0
-    BLOCK_DEVICE_STAT_FILE=""
-else
-    SECTOR_BYTES=$(cat "$BLOCK_DEVICE/queue/hw_sector_size")
-    BLOCK_DEVICE_STAT_FILE="$BLOCK_DEVICE/stat"
-fi
-
-
-# since getBlockDeviceIO looks at differences in stat file, run the
-# update so the first reported update has a sensible previous result to
-# compare to
-echo "0 0" > $TEMP_IO
-getBlockDeviceIO "$BLOCK_DEVICE_STAT_FILE" > /dev/null
-
-# same thing for getCpuUsage
-echo "0 0" > $TEMP_CPU
-getCpuUsage > /dev/null
-
-
-while true; do
-    runtimeInfo
-    sleep $SLEEP_TIME
-done

From 67a8453f80464d71d07268a37972b4cdf4021a02 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 19:23:33 -0400
Subject: [PATCH 11/49] fix

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl         | 4 ++--
 scripts/variantstore/wdl/extract/hail_gvs_import.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 7c765a9b417..9fca09980cd 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -125,8 +125,8 @@ workflow GvsUnifiedHail {
 
 task CreateVds {
     input {
-        File hail_gvs_import_script
         File hail_wheel
+        String hail_gvs_import_script
         String avro_prefix
         String vds_destination_path
     }
@@ -157,7 +157,7 @@ task CreateVds {
 
         export WORK=$PWD/work
         mkdir ${WORK}
-        python3 ~{hail_gvs_import_script} --avro_prefix ${AVRO} --write_prefix ${WORK} --references-dir ${REFERENCES}
+        python3 ~{hail_gvs_import_script} --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
 
         gcloud storage cp --recursive ${WORK}/gvs_export.vds ~{vds_destination_path}
     >>>
diff --git a/scripts/variantstore/wdl/extract/hail_gvs_import.py b/scripts/variantstore/wdl/extract/hail_gvs_import.py
index ade735dacc0..11fb138ac03 100644
--- a/scripts/variantstore/wdl/extract/hail_gvs_import.py
+++ b/scripts/variantstore/wdl/extract/hail_gvs_import.py
@@ -164,9 +164,9 @@ def args(key):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(allow_abbrev=False,
                                      description='Create base Hail VDS from exported GVS Avro files.')
-    parser.add_argument('--avro_prefix', type=str, help='Prefix under which exported GVS Avro files are found',
+    parser.add_argument('--avro-prefix', type=str, help='Prefix under which exported GVS Avro files are found',
                         default="@AVRO_PREFIX@")
-    parser.add_argument('--write_prefix', type=str,
+    parser.add_argument('--write-prefix', type=str,
                         help='Prefix to which VDS and temporary outputs should be written',
                         default="@WRITE_PREFIX@")
     parser.add_argument('--references-dir', type=str,

From 27f2690836c93db6634026aac2b2169c68e3cd79 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 19:28:18 -0400
Subject: [PATCH 12/49] cleanup

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 9fca09980cd..d913c257387 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -111,7 +111,7 @@ workflow GvsUnifiedHail {
 
     call CreateVds {
         input:
-            hail_gvs_import_script = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-GenerateHailScripts/hail_gvs_import.py",
+            hail_gvs_import_script = "https://raw.githubusercontent.com/broadinstitute/gatk/vs_639_hail_testing_spike/scripts/variantstore/wdl/extract/hail_gvs_import.py",
             hail_wheel = hail_wheel,
             avro_prefix = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/avro",
             vds_destination_path = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/gvs_export.vds"
@@ -135,6 +135,8 @@ task CreateVds {
         PS4='\D{+%F %T} \w $ '
         set -o errexit -o nounset -o pipefail -o xtrace
 
+        curl --silent --location --remote-name ~{hail_gvs_import_script}
+
         export AVRO=$PWD/avro
         mkdir -p ${AVRO}
 
@@ -157,7 +159,7 @@ task CreateVds {
 
         export WORK=$PWD/work
         mkdir ${WORK}
-        python3 ~{hail_gvs_import_script} --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
+        python3 ./hail_gvs_import.py --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
 
         gcloud storage cp --recursive ${WORK}/gvs_export.vds ~{vds_destination_path}
     >>>

From b4a0e964a9259ef70c813494741afaf32a7868de Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 19:38:59 -0400
Subject: [PATCH 13/49] oops

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index d913c257387..7bf465f82f2 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -140,7 +140,7 @@ task CreateVds {
         export AVRO=$PWD/avro
         mkdir -p ${AVRO}
 
-        gsutil ls -r ~{avro_prefix} | grep -E '\.avro$' | gcloud storage cp -I ${AVRO}
+        gcloud storage cp --recursive ~{avro_prefix} ${AVRO}
 
         export REFERENCES=$PWD/references
         mkdir -p ${REFERENCES}

From 1a3c10c262e581777e7bf5175dfe93e147302373 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 25 Oct 2022 19:46:35 -0400
Subject: [PATCH 14/49] fix

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 7bf465f82f2..5aa569a2822 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -137,10 +137,8 @@ task CreateVds {
 
         curl --silent --location --remote-name ~{hail_gvs_import_script}
 
-        export AVRO=$PWD/avro
-        mkdir -p ${AVRO}
-
-        gcloud storage cp --recursive ~{avro_prefix} ${AVRO}
+        # `avro_prefix` includes a trailing `avro`
+        gcloud storage cp --recursive ~{avro_prefix} $PWD
 
         export REFERENCES=$PWD/references
         mkdir -p ${REFERENCES}
@@ -159,6 +157,7 @@ task CreateVds {
 
         export WORK=$PWD/work
         mkdir ${WORK}
+        export AVRO=$PWD/avro
         python3 ./hail_gvs_import.py --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
 
         gcloud storage cp --recursive ${WORK}/gvs_export.vds ~{vds_destination_path}

From 23333c7cc1df706f6bfdfec88cc06eace4d97144 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 06:06:43 -0400
Subject: [PATCH 15/49] more spikey wip

---
 .../wdl/GvsQuickstartHailIntegration.wdl      | 234 +++++++++++++++++-
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   |  54 +++-
 .../wdl/extract/gvs_vds_tie_out.py            | 186 ++++++++++++++
 .../wdl/extract/hail_join_vds_vcfs.py         |  46 ++++
 4 files changed, 511 insertions(+), 9 deletions(-)
 create mode 100644 scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
 create mode 100644 scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index dc288005728..d45d1327a99 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -49,6 +49,236 @@ workflow GvsQuickstartHailIntegration {
                                         ]
 
         String drop_state = "FORTY"
+
+        Array[File] tieout_vcfs = [
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-14/0000000014-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-15/0000000015-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-16/0000000016-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-17/0000000017-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-18/0000000018-quickit.vcf.gz",
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+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-99/0000000099-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-100/0000000100-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz",
+                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz"
+                                  ]
+
+        Array[File] tieout_vcf_indexes = [
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+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz.tbi",
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+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-16/0000000016-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-17/0000000017-quickit.vcf.gz.tbi",
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+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-20/0000000020-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-21/0000000021-quickit.vcf.gz.tbi",
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+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz.tbi",
+                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz.tbi"
+                                         ]
     }
     String project_id = "gvs-internal"
 
@@ -67,7 +297,9 @@ workflow GvsQuickstartHailIntegration {
             input_vcfs = input_vcfs,
             input_vcf_indexes = input_vcf_indexes,
             filter_set_name = "quickit",
-            drop_state = drop_state
+            drop_state = "NONE",
+            tieout_vcfs = tieout_vcfs,
+            tieout_vcf_indexes = tieout_vcf_indexes,
     }
 
 #    call AssertIdenticalOutputs {
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 5aa569a2822..8f192e9347f 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -11,10 +11,10 @@ workflow GvsUnifiedHail {
         # Begin GvsAssignIds
         String dataset_name
         String project_id
-        String call_set_identifier
+        String branch_name
+        String call_set_identifier = branch_name
 
         Array[String] external_sample_names
-        String call_set_identifier
 
         File? gatk_override
         # End GvsAssignIds
@@ -49,6 +49,9 @@ workflow GvsUnifiedHail {
         # Begin CreateVds
         File hail_wheel = "gs://gvs-internal-scratch/hail-wheels/2022-10-18/0.2.102-964bee061eb0/hail-0.2.102-py3-none-any.whl"
         # End CreateVds
+
+        Array[File] tieout_vcfs
+        Array[File] tieout_vcf_indexes
     }
 
 #    call AssignIds.GvsAssignIds as AssignIds {
@@ -111,10 +114,12 @@ workflow GvsUnifiedHail {
 
     call CreateVds {
         input:
-            hail_gvs_import_script = "https://raw.githubusercontent.com/broadinstitute/gatk/vs_639_hail_testing_spike/scripts/variantstore/wdl/extract/hail_gvs_import.py",
+            branch_name = branch_name,
             hail_wheel = hail_wheel,
             avro_prefix = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/avro",
-            vds_destination_path = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/gvs_export.vds"
+            vds_destination_path = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/gvs_export.vds",
+            tieout_vcfs = tieout_vcfs,
+            tieout_vcf_indexes = tieout_vcf_indexes,
     }
 
     output {
@@ -126,18 +131,43 @@ workflow GvsUnifiedHail {
 task CreateVds {
     input {
         File hail_wheel
-        String hail_gvs_import_script
+        String branch_name
         String avro_prefix
         String vds_destination_path
+        Array[File] tieout_vcfs
+        Array[File] tieout_vcf_indexes
+    }
+    parameter_meta {
+        tieout_vcfs: {
+            localization_optional: true
+        }
+        tieout_vcf_indexes: {
+            localization_optional: true
+        }
     }
     command <<<
         # Prepend date, time and pwd to xtrace log entries.
         PS4='\D{+%F %T} \w $ '
         set -o errexit -o nounset -o pipefail -o xtrace
 
-        curl --silent --location --remote-name ~{hail_gvs_import_script}
+        script_url_prefix="https://raw.githubusercontent.com/broadinstitute/gatk/~{branch_name}/scripts/variantstore/wdl/extract"
+
+        for script in hail_gvs_import.py hail_join_vds_vcfs.py gvs_vds_tie_out.py
+        do
+            curl --silent --location --remote-name "${script_url_prefix}/${script}"
+        done
+
+        # Create a manifest of VCFs and indexes to bulk download with `gcloud storage cp`.
+        touch vcf_manifest.txt
+        for file in ~{sep=' ' tieout_vcfs} ~{sep=' ' tieout_vcf_indexes}
+        do
+            echo $file >> vcf_manifest.txt
+        done
 
-        # `avro_prefix` includes a trailing `avro`
+        # Copy VCFs and indexes to the current directory.
+        cat vcf_manifest.txt | gcloud storage cp -I .
+
+        # `avro_prefix` includes a trailing `avro` so don't add another `avro` here.
         gcloud storage cp --recursive ~{avro_prefix} $PWD
 
         export REFERENCES=$PWD/references
@@ -160,9 +190,17 @@ task CreateVds {
         export AVRO=$PWD/avro
         python3 ./hail_gvs_import.py --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
 
-        gcloud storage cp --recursive ${WORK}/gvs_export.vds ~{vds_destination_path}
+        export LOCAL_VDS_PATH=${WORK}/gvs_export.vds
+        export JOINED_MATRIX_TABLE_PATH=${WORK}/joined.mt
+
+        python3 ./hail_join_vds_vcfs.py --vds-path ${LOCAL_VDS_PATH} --joined-matrix-table-path ${JOINED_MATRIX_TABLE_PATH} *.vcf.gz
+
+        python3 ./gvs-vds-tie-out.py
+
+        gcloud storage cp --recursive ${LOCAL_VDS_PATH} ~{vds_destination_path}
     >>>
     runtime {
+        # `slim` here to be able to use Java
         docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-slim"
         disks: "local-disk 2000 HDD"
         memory: "30 GiB"
diff --git a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
new file mode 100644
index 00000000000..f8047c2eb09
--- /dev/null
+++ b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
@@ -0,0 +1,186 @@
+# gvs_vds_tie_out.py
+
+import hail as hl
+import pytest
+
+mt = hl.read_matrix_table('joined.mt')
+rs = mt.rows()
+cs = mt.cols()
+es = mt.entries()
+
+"""
+Schema of `mt`:
+----------------------------------------
+Global fields:
+    'tranche_data': array<struct {
+        model: str,
+        truth_sensitivity: float64,
+        min_vqslod: float64,
+        filter_name: str
+    }>
+    'truth_sensitivity_snp_threshold': float64
+    'truth_sensitivity_indel_threshold': float64
+    'snp_vqslod_threshold': float64
+    'indel_vqslod_threshold': float64
+----------------------------------------
+Column fields:
+    's': str
+    'vcf_col': struct {
+        s: str
+    }
+    'vds_col': struct {
+        s: str
+    }
+----------------------------------------
+Row fields:
+    'locus': locus<GRCh38>
+    'vcf_row': struct {
+        locus: locus<GRCh38>,
+        alleles: array<str>,
+        rsid: str,
+        qual: float64,
+        filters: set<str>,
+        info: struct {
+            AC: array<int32>,
+            AF: array<float64>,
+            AN: int32,
+            AS_QUALapprox: str,
+            AS_VQSLOD: array<str>,
+            AS_YNG: array<str>,
+            QUALapprox: int32
+        }
+    }
+    'vds_row': struct {
+        locus: locus<GRCh38>,
+        alleles: array<str>,
+        filters: set<str>,
+        as_vqsr: dict<str, struct {
+            model: str,
+            vqslod: float64,
+            yng_status: str
+        }>
+    }
+----------------------------------------
+Entry fields:
+    'vcf_entry': struct {
+        AD: array<int32>,
+        FT: str,
+        GQ: int32,
+        GT: call,
+        RGQ: int32
+    }
+    'vds_entry': struct {
+        LGT: call,
+        GQ: int32,
+        RGQ: int32,
+        LAD: array<int32>,
+        LA: array<int32>,
+        FT: bool
+    }
+----------------------------------------
+Column key: ['s']
+Row key: ['locus']
+----------------------------------------
+"""
+
+def updated_local_alleles(mt=mt):
+    """Creates field vds_entry.LA_vcf reindexing the VDS LA field to the VCF allele order"""
+    mt2 = mt.annotate_rows(vcf_allele_dict = hl.dict(hl.enumerate(mt.vcf_row.alleles, index_first=False)))
+    mt2 = mt2.annotate_rows(vds_allele_mapping = mt2.vds_row.alleles.map(lambda a: mt2.vcf_allele_dict[a]))
+    mt2 = mt2.annotate_entries(vds_entry = mt2.vds_entry.annotate(LA_vcf = mt2.vds_entry.LA.map(lambda i: mt2.vds_allele_mapping[i])))
+    return mt2
+
+def gq0_filter(mt=mt):
+    """Sets VDS LGTs to missing at reference genotypes when GQ is 0"""
+    mt2 = mt.annotate_entries(vds_entry = mt.vds_entry.annotate(LGT = hl.or_missing(mt.vds_entry.LGT.is_non_ref() | (mt.vds_entry.GQ > 0), mt.vds_entry.LGT)))
+    return mt2
+
+def ft_filter(mt=mt):
+    """Sets VDS LGTs to missing at non-ref genotypes when FT is False"""
+    mt2 = mt.annotate_entries(vds_entry = mt.vds_entry.annotate(LGT = hl.or_missing(hl.coalesce(mt.vds_entry.FT, True), mt.vds_entry.LGT)))
+    return mt2
+
+def find_violations(ht, predicate):
+    """Checks that `predicate` is true for all rows of `ht`.
+    Parameters
+    ----------
+    ht
+        Hail table.
+    predicate
+        Boolean expression in the row index of the `ht`.
+    """
+    ht=ht.annotate(CHECK = predicate)
+    violations = ht.aggregate(hl.agg.count_where(~ht.CHECK))
+    if violations > 0:
+        ht=ht.filter(~ht.CHECK)
+        ht.show()
+
+        assert False, f'{violations} violations'
+
+def test_locus_equivalence():
+    find_violations(rs, hl.is_defined(rs.vcf_row) & hl.is_defined(rs.vds_row))
+
+def test_sample_equivalence():
+    find_violations(cs, hl.is_defined(cs.vcf_col) & hl.is_defined(cs.vds_col))
+
+def test_allele_equivalence():
+    find_violations(rs, hl.set(rs.vcf_row.alleles) == hl.set(rs.vds_row.alleles))
+
+def test_filter_equivalence():
+    find_violations(rs, rs.vcf_row.filters == rs.vds_row.filters)
+
+def test_gt_equivalence():
+    es = updated_local_alleles().entries()
+    find_violations(es, hl.vds.lgt_to_gt(es.vds_entry.LGT, hl.coalesce(es.vds_entry.LA_vcf, [0])) == es.vcf_entry.GT)
+
+def test_gq_equivalence():
+    find_violations(es, es.vds_entry.GQ == es.vcf_entry.GQ)
+
+@pytest.mark.skip('bug in GATK, VCF wrong')
+def test_ad_equivalence():
+    es = updated_local_alleles().entries()
+
+    def lad_to_ad(lad, la, n_alleles):
+        return hl.rbind(hl.dict(hl.zip(la, lad)), lambda d: hl.range(n_alleles).map(lambda i: d.get(i, 0)))
+    es = es.annotate(vds_AD = lad_to_ad(es.vds_entry.LAD, hl.coalesce(es.vds_entry.LA_vcf, [0]), hl.len(es.vcf_row.alleles)))
+    find_violations(es, es.vds_AD == es.vcf_entry.AD)
+
+def test_ft_equivalence():
+    es = mt.filter_rows(hl.len(mt.vcf_row.filters) == 0).entries()
+    es2=es.filter(es.vcf_entry.GT.is_non_ref())
+    ft1 = es2.vds_entry.FT
+    ft2 = es2.vcf_entry.FT
+    find_violations(es2, hl.case()
+                    .when(hl.is_missing(ft1) != hl.is_missing(ft2), False)
+                    .when((ft1 == True) & (ft2 == 'PASS'), True)
+                    .when((ft1 == False) & (ft2 != 'PASS'), True)
+                    .default(False))
+
+
+def test_call_stats_equivalence():
+    mt = updated_local_alleles(ft_filter(gq0_filter()))
+    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    r = mt.rows()
+    find_violations(r, (r.vds_call_stats.AN == r.vcf_row.info.AN)
+                    & hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF, f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01)))
+                    & ((r.vds_call_stats.AC[1:] == r.vcf_row.info.AC)))
+
+
+def test_call_stats_equivalence_AN():
+    mt = updated_local_alleles(ft_filter(gq0_filter()))
+    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    r = mt.rows()
+    find_violations(r, (r.vds_call_stats.AN == r.vcf_row.info.AN))
+
+
+def test_call_stats_equivalence_AC():
+    mt = updated_local_alleles(ft_filter(gq0_filter()))
+    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    r = mt.rows()
+    find_violations(r, (r.vds_call_stats.AC[1:] == r.vcf_row.info.AC))
+
+def test_call_stats_equivalence_AF():
+    mt = updated_local_alleles(ft_filter(gq0_filter()))
+    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    r = mt.rows()
+    find_violations(r, hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF, f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01))))
diff --git a/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
new file mode 100644
index 00000000000..61950a3ca92
--- /dev/null
+++ b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
@@ -0,0 +1,46 @@
+import argparse
+import hail as hl
+
+
+def vds_mt(vds_path):
+    vds = hl.vds.read_vds(vds_path)
+    mt = hl.vds.to_dense_mt(vds)
+    vds_path='vds_dense.mt'
+    mt.write(vds_path, overwrite=True)
+    mt = hl.read_matrix_table(vds_path).key_rows_by('locus')
+    return mt
+
+
+def vcf_mt(vcf_paths):
+    mt = hl.import_vcf(vcf_paths, force_bgz=True, reference_genome='GRCh38')
+    return mt
+
+
+def joined_mt(mt_path):
+    joined = hl.experimental.full_outer_join_mt(vcf_mt, vds_mt)
+    joined = joined.rename({
+        'left_col' : 'vcf_col',
+        'right_col': 'vds_col',
+        'left_row' : 'vcf_row',
+        'right_row': 'vds_row',
+        'left_entry' : 'vcf_entry',
+        'right_entry': 'vds_entry',
+    })
+
+    joined.write(mt_path, overwrite=True)
+    mt = hl.read_matrix_table(mt_path)
+    return mt
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--vds-path', required=True,
+                        help='Input VDS for tieout')
+    parser.add_argument('--joined-matrix-table-path', required=True, help='Output joined MatrixTable')
+    parser.add_argument('vcf_paths', required=True, nargs='+')
+
+    vds_mt = vds_mt(parser.vds_path)
+    vcf_mt = vcf_mt(parser.vcf_paths)
+    joined_mt(parser.joined_matrix_table_path)
+
+

From 1834e5ff48f95de5bcbb481e0ffb8bbc3a40cfcf Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 07:36:27 -0400
Subject: [PATCH 16/49] wip

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   |  7 +-
 .../wdl/extract/gvs_vds_tie_out.py            | 66 +++++++++++++------
 .../wdl/extract/hail_join_vds_vcfs.py         | 14 ++--
 3 files changed, 60 insertions(+), 27 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 8f192e9347f..0785d2039b2 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -195,9 +195,12 @@ task CreateVds {
 
         python3 ./hail_join_vds_vcfs.py --vds-path ${LOCAL_VDS_PATH} --joined-matrix-table-path ${JOINED_MATRIX_TABLE_PATH} *.vcf.gz
 
-        python3 ./gvs-vds-tie-out.py
-
+        # Copy up the VDS
         gcloud storage cp --recursive ${LOCAL_VDS_PATH} ~{vds_destination_path}
+
+        pip install pytest
+        ln ${WORK}/joined.mt .
+        pytest ./gvs_vds_tie_out.py
     >>>
     runtime {
         # `slim` here to be able to use Java
diff --git a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
index f8047c2eb09..6ff70b1dc53 100644
--- a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
+++ b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
@@ -8,6 +8,7 @@
 cs = mt.cols()
 es = mt.entries()
 
+
 """
 Schema of `mt`:
 ----------------------------------------
@@ -83,23 +84,30 @@
 ----------------------------------------
 """
 
+
 def updated_local_alleles(mt=mt):
     """Creates field vds_entry.LA_vcf reindexing the VDS LA field to the VCF allele order"""
-    mt2 = mt.annotate_rows(vcf_allele_dict = hl.dict(hl.enumerate(mt.vcf_row.alleles, index_first=False)))
-    mt2 = mt2.annotate_rows(vds_allele_mapping = mt2.vds_row.alleles.map(lambda a: mt2.vcf_allele_dict[a]))
-    mt2 = mt2.annotate_entries(vds_entry = mt2.vds_entry.annotate(LA_vcf = mt2.vds_entry.LA.map(lambda i: mt2.vds_allele_mapping[i])))
+    mt2 = mt.annotate_rows(vcf_allele_dict=hl.dict(hl.enumerate(mt.vcf_row.alleles, index_first=False)))
+    mt2 = mt2.annotate_rows(vds_allele_mapping=mt2.vds_row.alleles.map(lambda a: mt2.vcf_allele_dict[a]))
+    mt2 = mt2.annotate_entries(
+        vds_entry=mt2.vds_entry.annotate(LA_vcf=mt2.vds_entry.LA.map(lambda i: mt2.vds_allele_mapping[i])))
     return mt2
 
+
 def gq0_filter(mt=mt):
     """Sets VDS LGTs to missing at reference genotypes when GQ is 0"""
-    mt2 = mt.annotate_entries(vds_entry = mt.vds_entry.annotate(LGT = hl.or_missing(mt.vds_entry.LGT.is_non_ref() | (mt.vds_entry.GQ > 0), mt.vds_entry.LGT)))
+    mt2 = mt.annotate_entries(vds_entry=mt.vds_entry.annotate(
+        LGT=hl.or_missing(mt.vds_entry.LGT.is_non_ref() | (mt.vds_entry.GQ > 0), mt.vds_entry.LGT)))
     return mt2
 
+
 def ft_filter(mt=mt):
     """Sets VDS LGTs to missing at non-ref genotypes when FT is False"""
-    mt2 = mt.annotate_entries(vds_entry = mt.vds_entry.annotate(LGT = hl.or_missing(hl.coalesce(mt.vds_entry.FT, True), mt.vds_entry.LGT)))
+    mt2 = mt.annotate_entries(
+        vds_entry=mt.vds_entry.annotate(LGT=hl.or_missing(hl.coalesce(mt.vds_entry.FT, True), mt.vds_entry.LGT)))
     return mt2
 
+
 def find_violations(ht, predicate):
     """Checks that `predicate` is true for all rows of `ht`.
     Parameters
@@ -109,45 +117,54 @@ def find_violations(ht, predicate):
     predicate
         Boolean expression in the row index of the `ht`.
     """
-    ht=ht.annotate(CHECK = predicate)
+    ht = ht.annotate(CHECK=predicate)
     violations = ht.aggregate(hl.agg.count_where(~ht.CHECK))
     if violations > 0:
-        ht=ht.filter(~ht.CHECK)
+        ht = ht.filter(~ht.CHECK)
         ht.show()
 
         assert False, f'{violations} violations'
 
+
 def test_locus_equivalence():
     find_violations(rs, hl.is_defined(rs.vcf_row) & hl.is_defined(rs.vds_row))
 
+
 def test_sample_equivalence():
     find_violations(cs, hl.is_defined(cs.vcf_col) & hl.is_defined(cs.vds_col))
 
+
 def test_allele_equivalence():
     find_violations(rs, hl.set(rs.vcf_row.alleles) == hl.set(rs.vds_row.alleles))
 
+
 def test_filter_equivalence():
     find_violations(rs, rs.vcf_row.filters == rs.vds_row.filters)
 
+
 def test_gt_equivalence():
     es = updated_local_alleles().entries()
     find_violations(es, hl.vds.lgt_to_gt(es.vds_entry.LGT, hl.coalesce(es.vds_entry.LA_vcf, [0])) == es.vcf_entry.GT)
 
+
 def test_gq_equivalence():
     find_violations(es, es.vds_entry.GQ == es.vcf_entry.GQ)
 
-@pytest.mark.skip('bug in GATK, VCF wrong')
+
 def test_ad_equivalence():
     es = updated_local_alleles().entries()
 
     def lad_to_ad(lad, la, n_alleles):
         return hl.rbind(hl.dict(hl.zip(la, lad)), lambda d: hl.range(n_alleles).map(lambda i: d.get(i, 0)))
-    es = es.annotate(vds_AD = lad_to_ad(es.vds_entry.LAD, hl.coalesce(es.vds_entry.LA_vcf, [0]), hl.len(es.vcf_row.alleles)))
+
+    es = es.annotate(
+        vds_AD=lad_to_ad(es.vds_entry.LAD, hl.coalesce(es.vds_entry.LA_vcf, [0]), hl.len(es.vcf_row.alleles)))
     find_violations(es, es.vds_AD == es.vcf_entry.AD)
 
+
 def test_ft_equivalence():
     es = mt.filter_rows(hl.len(mt.vcf_row.filters) == 0).entries()
-    es2=es.filter(es.vcf_entry.GT.is_non_ref())
+    es2 = es.filter(es.vcf_entry.GT.is_non_ref())
     ft1 = es2.vds_entry.FT
     ft2 = es2.vcf_entry.FT
     find_violations(es2, hl.case()
@@ -159,28 +176,39 @@ def test_ft_equivalence():
 
 def test_call_stats_equivalence():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
-    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    mt = mt.annotate_rows(
+        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
+                                         hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, (r.vds_call_stats.AN == r.vcf_row.info.AN)
-                    & hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF, f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01)))
+                    & hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF,
+                                                       f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01)))
                     & ((r.vds_call_stats.AC[1:] == r.vcf_row.info.AC)))
 
 
-def test_call_stats_equivalence_AN():
+def test_call_stats_equivalence_an():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
-    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    mt = mt.annotate_rows(
+        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
+                                         hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, (r.vds_call_stats.AN == r.vcf_row.info.AN))
 
 
-def test_call_stats_equivalence_AC():
+def test_call_stats_equivalence_ac():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
-    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    mt = mt.annotate_rows(
+        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
+                                         hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, (r.vds_call_stats.AC[1:] == r.vcf_row.info.AC))
 
-def test_call_stats_equivalence_AF():
+
+def test_call_stats_equivalence_af():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
-    mt = mt.annotate_rows(vds_call_stats = hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])), hl.len(mt.vds_row.alleles)))
+    mt = mt.annotate_rows(
+        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
+                                         hl.len(mt.vds_row.alleles)))
     r = mt.rows()
-    find_violations(r, hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF, f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01))))
+    find_violations(r, hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF,
+                                                        f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01))))
diff --git a/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
index 61950a3ca92..6b62b046cbc 100644
--- a/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
+++ b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
@@ -5,14 +5,14 @@
 def vds_mt(vds_path):
     vds = hl.vds.read_vds(vds_path)
     mt = hl.vds.to_dense_mt(vds)
-    vds_path='vds_dense.mt'
+    vds_path = 'vds_dense.mt'
     mt.write(vds_path, overwrite=True)
     mt = hl.read_matrix_table(vds_path).key_rows_by('locus')
     return mt
 
 
 def vcf_mt(vcf_paths):
-    mt = hl.import_vcf(vcf_paths, force_bgz=True, reference_genome='GRCh38')
+    mt = hl.import_vcf(vcf_paths, force_bgz=True, reference_genome='GRCh38').key_rows_by('locus')
     return mt
 
 
@@ -37,10 +37,12 @@ def joined_mt(mt_path):
     parser.add_argument('--vds-path', required=True,
                         help='Input VDS for tieout')
     parser.add_argument('--joined-matrix-table-path', required=True, help='Output joined MatrixTable')
-    parser.add_argument('vcf_paths', required=True, nargs='+')
+    parser.add_argument('vcf_paths', nargs='+')
 
-    vds_mt = vds_mt(parser.vds_path)
-    vcf_mt = vcf_mt(parser.vcf_paths)
-    joined_mt(parser.joined_matrix_table_path)
+    args = parser.parse_args()
+
+    vds_mt = vds_mt(args.vds_path)
+    vcf_mt = vcf_mt(args.vcf_paths)
+    joined_mt(args.joined_matrix_table_path)
 
 

From 4daa85e296aa62d28940c789bee4057c255404c9 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 07:42:37 -0400
Subject: [PATCH 17/49] oops

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index d45d1327a99..10d86066bb4 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -290,7 +290,7 @@ workflow GvsQuickstartHailIntegration {
 
     call Unified.GvsUnifiedHail {
         input:
-            call_set_identifier = branch_name,
+            branch_name = branch_name,
             dataset_name = "quickit_vs_639_hail_testing_spike_80af46a",
             project_id = project_id,
             external_sample_names = external_sample_names,

From f3a40849bb017931644c67f7b3341a3726d603a8 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 08:14:38 -0400
Subject: [PATCH 18/49] gah

---
 scripts/variantstore/wdl/GvsUnifiedHail.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 0785d2039b2..59acf8b234c 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -199,7 +199,7 @@ task CreateVds {
         gcloud storage cp --recursive ${LOCAL_VDS_PATH} ~{vds_destination_path}
 
         pip install pytest
-        ln ${WORK}/joined.mt .
+        ln -s ${WORK}/joined.mt .
         pytest ./gvs_vds_tie_out.py
     >>>
     runtime {

From b7ca91d450559211eb60ff33d6d0bf2d59ea8597 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 13:53:42 -0400
Subject: [PATCH 19/49] revert many of the differences with non-hail
 integration test

---
 .../wdl/GvsExtractAvroFilesForHail.wdl        |   1 +
 .../wdl/GvsQuickstartHailIntegration.wdl      | 310 +++---------------
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   | 190 +++++++----
 3 files changed, 172 insertions(+), 329 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl b/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
index b1d780bd1b3..4bba71c214e 100644
--- a/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
+++ b/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
@@ -62,6 +62,7 @@ workflow GvsExtractAvroFilesForHail {
         String vds_output_path = GenerateHailScripts.vds_output_path
         String sites_only_vcf_output_path = GenerateHailScripts.sites_only_vcf_output_path
         String vat_inputs_output_path = GenerateHailScripts.vat_inputs_output_path
+        String avro_prefix = ExtractFromNonSuperpartitionedTables.output_prefix
     }
 }
 
diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 10d86066bb4..f8561b3cf32 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -7,7 +7,7 @@ workflow GvsQuickstartHailIntegration {
 
     input {
         String branch_name
-        String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-07-05/"
+        String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-10-20/"
 
         Array[String] external_sample_names = [
                                               "ERS4367795",
@@ -48,284 +48,64 @@ workflow GvsQuickstartHailIntegration {
                                         "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi"
                                         ]
 
-        String drop_state = "FORTY"
-
-        Array[File] tieout_vcfs = [
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-14/0000000014-quickit.vcf.gz",
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-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz",
-                                  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz"
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-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz.tbi",
-                                         "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/1cfae8ea-2e3b-4ba2-b6db-802349ef69bc/GvsQuickstartIntegration/b270ddee-1bc8-4488-bc60-79d0cb82797e/call-GvsUnified/GvsUnified/1a15df10-9020-4c50-aa61-55f241ebb874/call-GvsExtractCallset/GvsExtractCallset/ce4cced0-9863-4887-8a35-a85c8bf7b89a/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz.tbi"
-                                         ]
+        Int? extract_scatter_count
+        String drop_state = "NONE"
+
     }
     String project_id = "gvs-internal"
 
-#    call Utils.BuildGATKJarAndCreateDataset {
-#        input:
-#            branch_name = branch_name,
-#            dataset_prefix = "quickit"
-#    }
+    call Utils.BuildGATKJarAndCreateDataset {
+        input:
+            branch_name = branch_name,
+            dataset_prefix = "quickit"
+    }
 
     call Unified.GvsUnifiedHail {
         input:
-            branch_name = branch_name,
-            dataset_name = "quickit_vs_639_hail_testing_spike_80af46a",
+            call_set_identifier = branch_name,
+            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
             project_id = project_id,
             external_sample_names = external_sample_names,
+            gatk_override = BuildGATKJarAndCreateDataset.jar,
             input_vcfs = input_vcfs,
             input_vcf_indexes = input_vcf_indexes,
             filter_set_name = "quickit",
-            drop_state = "NONE",
-            tieout_vcfs = tieout_vcfs,
-            tieout_vcf_indexes = tieout_vcf_indexes,
+            extract_table_prefix = "quickit",
+            extract_scatter_count = extract_scatter_count,
+            # Force filtering off as it is not deterministic and the initial version of this integration test does not
+            # allow for inexact matching of actual and expected results.
+            extract_do_not_filter_override = true,
+            drop_state = drop_state,
+    }
+
+    call AssertIdenticalOutputs {
+        input:
+            expected_output_prefix = expected_output_prefix,
+            actual_vcfs = GvsUnifiedHail.output_vcfs
+    }
+
+    call AssertCostIsTrackedAndExpected {
+        input:
+            go = GvsUnifiedHail.done,
+            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+            project_id = project_id,
+            expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
+    }
+
+    call AssertTableSizesAreExpected {
+        input:
+            go = GvsUnifiedHail.done,
+            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+            project_id = project_id,
+            expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
     }
 
-#    call AssertIdenticalOutputs {
-#        input:
-#            expected_output_prefix = expected_output_prefix,
-#            actual_vcfs = GvsUnified.output_vcfs
-#    }
-#
-#    call AssertCostIsTrackedAndExpected {
-#        input:
-#            go = GvsUnified.done,
-#            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-#            project_id = project_id,
-#            expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
-#    }
-#
-#    call AssertTableSizesAreExpected {
-#        input:
-#            go = GvsUnified.done,
-#            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-#            project_id = project_id,
-#            expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
-#    }
-#
     output {
-        # String vds_output_path = GvsUnifiedHail.vds_output_path
+        Array[File] output_vcfs = GvsUnifiedHail.output_vcfs
+        Array[File] output_vcf_indexes = GvsUnifiedHail.output_vcf_indexes
+        Float total_vcfs_size_mb = GvsUnifiedHail.total_vcfs_size_mb
+        File manifest = GvsUnifiedHail.manifest
+        String vds_output_path = GvsUnifiedHail.vds_output_path
         Boolean done = true
     }
 }
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 59acf8b234c..5e76c1b4620 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -46,85 +46,147 @@ workflow GvsUnifiedHail {
         Int? SNP_VQSR_mem_gb_override
         # End GvsCreateFilterSet
 
+        # Begin GvsPrepareRangesCallset
+        String extract_table_prefix
+
+        String query_project = project_id
+        String destination_project = project_id
+        String destination_dataset = dataset_name
+        String fq_temp_table_dataset = "~{destination_project}.~{destination_dataset}"
+
+        Array[String]? query_labels
+        File? sample_names_to_extract
+        # End GvsPrepareRangesCallset
+
+        # Begin GvsExtractCallset
+        Int? extract_scatter_count
+
+        File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
+
+        String extract_output_file_base_name = sub(filter_set_name, " ", "-")
+
+        Int? extract_maxretries_override
+        Int? extract_preemptible_override
+        String? extract_output_gcs_dir
+        Int? split_intervals_disk_size_override
+        Int? split_intervals_mem_override
+        Boolean extract_do_not_filter_override = false
+        # End GvsExtractCallset
+
         # Begin CreateVds
         File hail_wheel = "gs://gvs-internal-scratch/hail-wheels/2022-10-18/0.2.102-964bee061eb0/hail-0.2.102-py3-none-any.whl"
         # End CreateVds
+    }
 
-        Array[File] tieout_vcfs
-        Array[File] tieout_vcf_indexes
+    call AssignIds.GvsAssignIds as AssignIds {
+        input:
+            dataset_name = dataset_name,
+            project_id = project_id,
+            external_sample_names = external_sample_names,
+            assign_ids_gatk_override = gatk_override
+    }
+
+    call ImportGenomes.GvsImportGenomes {
+        input:
+            go = AssignIds.done,
+            dataset_name = dataset_name,
+            project_id = project_id,
+            external_sample_names = external_sample_names,
+            input_vcfs = input_vcfs,
+            input_vcf_indexes = input_vcf_indexes,
+            interval_list = interval_list,
+            load_data_preemptible_override = load_data_preemptible_override,
+            load_data_maxretries_override = load_data_maxretries_override,
+            load_data_gatk_override = gatk_override,
+            load_data_batch_size = load_data_batch_size,
+            drop_state = drop_state
     }
 
-#    call AssignIds.GvsAssignIds as AssignIds {
-#        input:
-#            dataset_name = dataset_name,
-#            project_id = project_id,
-#            external_sample_names = external_sample_names,
-#            assign_ids_gatk_override = gatk_override
-#    }
-#
-#    call ImportGenomes.GvsImportGenomes {
-#        input:
-#            go = AssignIds.done,
-#            dataset_name = dataset_name,
-#            project_id = project_id,
-#            external_sample_names = external_sample_names,
-#            input_vcfs = input_vcfs,
-#            input_vcf_indexes = input_vcf_indexes,
-#            interval_list = interval_list,
-#            load_data_preemptible_override = load_data_preemptible_override,
-#            load_data_maxretries_override = load_data_maxretries_override,
-#            load_data_gatk_override = gatk_override,
-#            load_data_batch_size = load_data_batch_size,
-#            drop_state = drop_state
-#    }
-#
-#    call PopulateAltAllele.GvsPopulateAltAllele {
-#        input:
-#            call_set_identifier = call_set_identifier,
-#            go = GvsImportGenomes.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,
-#            indel_recalibration_annotation_values = indel_recalibration_annotation_values,
-#            snp_recalibration_annotation_values = snp_recalibration_annotation_values,
-#            interval_list = interval_list,
-#            gatk_override = gatk_override,
-#            INDEL_VQSR_max_gaussians_override = INDEL_VQSR_max_gaussians_override,
-#            INDEL_VQSR_mem_gb_override = INDEL_VQSR_mem_gb_override,
-#            SNP_VQSR_max_gaussians_override = SNP_VQSR_max_gaussians_override,
-#            SNP_VQSR_mem_gb_override = SNP_VQSR_mem_gb_override
-#    }
-#
-#    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
-#        input:
-#            go = GvsCreateFilterSet.done,
-#            project_id = project_id,
-#            dataset = dataset_name,
-#            filter_set_name = filter_set_name,
-#            scatter_width = 10,
-#    }
+    call PopulateAltAllele.GvsPopulateAltAllele {
+        input:
+            call_set_identifier = call_set_identifier,
+            go = GvsImportGenomes.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,
+            indel_recalibration_annotation_values = indel_recalibration_annotation_values,
+            snp_recalibration_annotation_values = snp_recalibration_annotation_values,
+            interval_list = interval_list,
+            gatk_override = gatk_override,
+            INDEL_VQSR_max_gaussians_override = INDEL_VQSR_max_gaussians_override,
+            INDEL_VQSR_mem_gb_override = INDEL_VQSR_mem_gb_override,
+            SNP_VQSR_max_gaussians_override = SNP_VQSR_max_gaussians_override,
+            SNP_VQSR_mem_gb_override = SNP_VQSR_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
+    }
+
+    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
+        input:
+            go = GvsCreateFilterSet.done,
+            project_id = project_id,
+            dataset = dataset_name,
+            filter_set_name = filter_set_name,
+            scatter_width = 10,
+    }
 
     call CreateVds {
         input:
             branch_name = branch_name,
             hail_wheel = hail_wheel,
-            avro_prefix = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/avro",
-            vds_destination_path = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/e7e3bf72-c849-4845-b0c2-f324569afb69/GvsQuickstartHailIntegration/e23f1bd3-29b5-43b2-bd53-f22f1e1509d5/call-GvsUnifiedHail/GvsUnifiedHail/a783025e-e639-42e7-981c-cc7ff4d923de/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/94a25fb5-5913-4432-9c2a-f1efdc0160f8/call-OutputPath/gvs_export.vds",
-            tieout_vcfs = tieout_vcfs,
-            tieout_vcf_indexes = tieout_vcf_indexes,
+            avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
+            vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
+            tieout_vcfs = GvsExtractCallset.output_vcfs,
+            tieout_vcf_indexes = GvsExtractCallset.output_vcf_indexes,
     }
 
     output {
         Boolean done = true
-        # String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
+        String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
     }
 }
 

From d1d71b080cfcb785d9553dd331fe13501982b14b Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 14:24:48 -0400
Subject: [PATCH 20/49] fixes

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 2 +-
 scripts/variantstore/wdl/GvsUnified.wdl                   | 1 -
 scripts/variantstore/wdl/GvsUnifiedHail.wdl               | 8 ++++++++
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index f8561b3cf32..623eade6b3a 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -62,7 +62,7 @@ workflow GvsQuickstartHailIntegration {
 
     call Unified.GvsUnifiedHail {
         input:
-            call_set_identifier = branch_name,
+            branch_name = branch_name,
             dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
             project_id = project_id,
             external_sample_names = external_sample_names,
diff --git a/scripts/variantstore/wdl/GvsUnified.wdl b/scripts/variantstore/wdl/GvsUnified.wdl
index 2fb2605c4bd..89989a0dae2 100644
--- a/scripts/variantstore/wdl/GvsUnified.wdl
+++ b/scripts/variantstore/wdl/GvsUnified.wdl
@@ -15,7 +15,6 @@ workflow GvsUnified {
         String call_set_identifier
 
         Array[String] external_sample_names
-        String call_set_identifier
 
         File? gatk_override
         # End GvsAssignIds
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
index 5e76c1b4620..ff800649f93 100644
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
@@ -4,6 +4,8 @@ import "GvsAssignIds.wdl" as AssignIds
 import "GvsImportGenomes.wdl" as ImportGenomes
 import "GvsPopulateAltAllele.wdl" as PopulateAltAllele
 import "GvsCreateFilterSet.wdl" as CreateFilterSet
+import "GvsPrepareRangesCallset.wdl" as PrepareRangesCallset
+import "GvsExtractCallset.wdl" as ExtractCallset
 import "GvsExtractAvroFilesForHail.wdl" as ExtractAvroFilesForHail
 
 workflow GvsUnifiedHail {
@@ -186,6 +188,12 @@ workflow GvsUnifiedHail {
 
     output {
         Boolean done = true
+        Array[File] output_vcfs = GvsExtractCallset.output_vcfs
+        Array[File] output_vcf_indexes = GvsExtractCallset.output_vcf_indexes
+        Float total_vcfs_size_mb = GvsExtractCallset.total_vcfs_size_mb
+        Array[File] output_vcf_interval_files = GvsExtractCallset.output_vcf_interval_files
+        File? sample_name_list = GvsExtractCallset.sample_name_list
+        File manifest = GvsExtractCallset.manifest
         String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
     }
 }

From c85d452865e6f22b224368c6e138172e3f8481fd Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 15:02:52 -0400
Subject: [PATCH 21/49] so much DRYing

---
 .dockstore.yml                                |   8 -
 .../wdl/GvsQuickstartHailIntegration.wdl      | 376 ++++--------------
 .../wdl/GvsQuickstartIntegration.wdl          |   2 +
 scripts/variantstore/wdl/GvsUnifiedHail.wdl   | 284 -------------
 4 files changed, 83 insertions(+), 587 deletions(-)
 delete mode 100644 scripts/variantstore/wdl/GvsUnifiedHail.wdl

diff --git a/.dockstore.yml b/.dockstore.yml
index 00407d8647b..b1580b28f0b 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -180,14 +180,6 @@ workflows:
        branches:
          - master
          - ah_var_store
-   - name: GvsUnifiedHail
-     subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsUnifiedHail.wdl
-     filters:
-       branches:
-         - master
-         - ah_var_store
-         - vs_639_hail_testing_spike
    - name: GvsJointVariantCalling
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl
diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 623eade6b3a..9d226a7e842 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -1,347 +1,133 @@
 version 1.0
 
-import "GvsUnifiedHail.wdl" as Unified
 import "GvsUtils.wdl" as Utils
+import "GvsExtractAvroFilesForHail.wdl" as ExtractAvroFilesForHail
+import "GvsQuickstartIntegration.wdl" as QuickstartVCFIntegration
 
 workflow GvsQuickstartHailIntegration {
-
     input {
         String branch_name
-        String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-10-20/"
-
-        Array[String] external_sample_names = [
-                                              "ERS4367795",
-                                              "ERS4367796",
-                                              "ERS4367797",
-                                              "ERS4367798",
-                                              "ERS4367799",
-                                              "ERS4367800",
-                                              "ERS4367801",
-                                              "ERS4367803",
-                                              "ERS4367804",
-                                              "ERS4367805"
-                                              ]
-
-        Array[File] input_vcfs = [
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz"
-                                 ]
-
-        Array[File] input_vcf_indexes = [
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi"
-                                        ]
-
-        Int? extract_scatter_count
-        String drop_state = "NONE"
-
+        String hail_wheel = "gs://gvs-internal-scratch/hail-wheels/2022-10-18/0.2.102-964bee061eb0/hail-0.2.102-py3-none-any.whl"
     }
-    String project_id = "gvs-internal"
 
-    call Utils.BuildGATKJarAndCreateDataset {
-        input:
-            branch_name = branch_name,
-            dataset_prefix = "quickit"
-    }
+    String project_id = "gvs-internal"
 
-    call Unified.GvsUnifiedHail {
+    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
         input:
             branch_name = branch_name,
-            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-            project_id = project_id,
-            external_sample_names = external_sample_names,
-            gatk_override = BuildGATKJarAndCreateDataset.jar,
-            input_vcfs = input_vcfs,
-            input_vcf_indexes = input_vcf_indexes,
-            filter_set_name = "quickit",
-            extract_table_prefix = "quickit",
-            extract_scatter_count = extract_scatter_count,
-            # Force filtering off as it is not deterministic and the initial version of this integration test does not
-            # allow for inexact matching of actual and expected results.
-            extract_do_not_filter_override = true,
-            drop_state = drop_state,
-    }
-
-    call AssertIdenticalOutputs {
-        input:
-            expected_output_prefix = expected_output_prefix,
-            actual_vcfs = GvsUnifiedHail.output_vcfs
     }
 
-    call AssertCostIsTrackedAndExpected {
+    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
         input:
-            go = GvsUnifiedHail.done,
-            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+            go = QuickstartVCFIntegration.done,
             project_id = project_id,
-            expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
+            dataset = QuickstartVCFIntegration.dataset_name,
+            filter_set_name = QuickstartVCFIntegration.filter_set_name,
+            scatter_width = 10,
     }
 
-    call AssertTableSizesAreExpected {
+    call CreateVds {
         input:
-            go = GvsUnifiedHail.done,
-            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-            project_id = project_id,
-            expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
+            branch_name = branch_name,
+            hail_wheel = hail_wheel,
+            avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
+            vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
+            tieout_vcfs = QuickstartVCFIntegration.output_vcfs,
+            tieout_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes,
     }
 
     output {
-        Array[File] output_vcfs = GvsUnifiedHail.output_vcfs
-        Array[File] output_vcf_indexes = GvsUnifiedHail.output_vcf_indexes
-        Float total_vcfs_size_mb = GvsUnifiedHail.total_vcfs_size_mb
-        File manifest = GvsUnifiedHail.manifest
-        String vds_output_path = GvsUnifiedHail.vds_output_path
+        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
+        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
+        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
+        File manifest = QuickstartVCFIntegration.manifest
+        String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
         Boolean done = true
     }
 }
 
 
-task AssertIdenticalOutputs {
+task CreateVds {
     input {
-        String expected_output_prefix
-        Array[File] actual_vcfs
+        File hail_wheel
+        String branch_name
+        String avro_prefix
+        String vds_destination_path
+        Array[File] tieout_vcfs
+        Array[File] tieout_vcf_indexes
+    }
+    parameter_meta {
+        tieout_vcfs: {
+             localization_optional: true
+         }
+        tieout_vcf_indexes: {
+            localization_optional: true
+        }
     }
-
     command <<<
-        set -o errexit
-        set -o nounset
-        set -o pipefail
-
-        failures=()
-
-        # Where the current set of expected results lives in the cloud
-        expected_prefix="~{expected_output_prefix}"
-        # Remove a trailing slash if there is one
-        expected_prefix=${expected_prefix%/}
+        # Prepend date, time and pwd to xtrace log entries.
+        PS4='\D{+%F %T} \w $ '
+        set -o errexit -o nounset -o pipefail -o xtrace
 
-        # Download all the expected data
-        mkdir expected
-        cd expected
-        # Make a FOFN for more efficient downloading
-        for file in ~{sep= ' ' actual_vcfs}; do
-            echo "$expected_prefix/$(basename $file)" >> expected_fofn.txt
-        done
-        # Download and unzip all the expected data
-        cat expected_fofn.txt | gsutil -m cp -I .
-        gzip -d *.gz
-        cd ..
-
-        # Also unzip actual result data
-        gzip -d ~{sep= ' ' actual_vcfs}
+        script_url_prefix="https://raw.githubusercontent.com/broadinstitute/gatk/~{branch_name}/scripts/variantstore/wdl/extract"
 
-        # Headers first, these can yield useful diagnostics when there are mismatches.
-        for file in ~{sep=' ' actual_vcfs}; do
-          unzipped=${file%.gz}
-          expected="expected/$(basename $unzipped)"
-          set +o errexit
-          cmp <(grep '^#' $unzipped) <(grep '^#' $expected)
-          rc=$?
-          set -o errexit
-          if [[ $rc -ne 0 ]]; then
-            # If there is a mismatch add it to a list of failures but keep on looking for mismatches.
-            failures+=( $unzipped )
-          fi
+        for script in hail_gvs_import.py hail_join_vds_vcfs.py gvs_vds_tie_out.py
+        do
+        curl --silent --location --remote-name "${script_url_prefix}/${script}"
         done
 
-        if [[ ${#failures[@]} -ne 0 ]]; then
-          echo "Error: headers for the following files do not match:"
-          for failure in ${failures[@]}; do
-            echo $(basename $failure)
-            expected="expected/$(basename $failure)"
-            diff $failure $expected
-          done
-          exit 1
-        fi
-
-        # If the headers all matched look for any mismatches in overall file content.
-        fail=0
-        for file in ~{sep=' ' actual_vcfs}; do
-          unzipped=${file%.gz}
-          expected="expected/$(basename $unzipped)"
-          set +o errexit
-          cmp $unzipped $expected
-          rc=$?
-          set -o errexit
-          if [[ $rc -ne 0 ]]; then
-            echo "Error: file contents of expected and actual do not match: $(basename $unzipped)"
-            fail=1
-          fi
+        # Create a manifest of VCFs and indexes to bulk download with `gcloud storage cp`.
+        touch vcf_manifest.txt
+        for file in ~{sep=' ' tieout_vcfs} ~{sep=' ' tieout_vcf_indexes}
+        do
+        echo $file >> vcf_manifest.txt
         done
 
-        if [[ $fail -ne 0 ]]; then
-          exit 1
-        fi
-
-        echo "All vcfs compared and matched!"
-    >>>
-
-    runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
-        disks: "local-disk 500 HDD"
-    }
-
-    output {
-        File fofn = "expected/expected_fofn.txt"
-        Boolean done = true
-    }
-}
-
-task AssertCostIsTrackedAndExpected {
-    meta {
-        # we want to check the database each time this runs
-        volatile: true
-    }
-
-    input {
-        Boolean go = true
-        String dataset_name
-        String project_id
-        File expected_output_csv
-    }
-
-    command <<<
-        set -o errexit
-        set -o nounset
-        set -o pipefail
-
-        echo "project_id = ~{project_id}" > ~/.bigqueryrc
-        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
-            "SELECT call, step, event_key, sum(event_bytes) \
-              FROM \`~{dataset_name}.cost_observability\` \
-              GROUP BY call, step, event_key \
-              ORDER BY call, step, event_key" > cost_observability_output.csv
+        # Copy VCFs and indexes to the current directory.
+        cat vcf_manifest.txt | gcloud storage cp -I .
 
-        # Put the exit code in a file because we are using a subshell (while) later and changes to the variable *in* the subshell are lost
-        echo "0" > ret_val.txt
+        # `avro_prefix` includes a trailing `avro` so don't add another `avro` here.
+        gcloud storage cp --recursive ~{avro_prefix} $PWD
 
-        paste cost_observability_output.csv ~{expected_output_csv} | while  IFS=$'\t' read observed expected; do
-        IFS=, read -ra OBS <<< "$observed"
-        IFS=, read -ra EXP <<< "$expected"
-        if [[ "${#OBS[@]}" -ne 4  || "${#EXP[@]}" -ne 4 ]]; then
-          echo "Unexpected number of rows found in the input files"
-          exit 1
-        fi
+        export REFERENCES=$PWD/references
+        mkdir -p ${REFERENCES}
 
-        OBS_KEY=${OBS[0]}.${OBS[1]}.${OBS[2]}
-        EXP_KEY=${EXP[0]}.${EXP[1]}.${EXP[2]}
-        if [[ "$OBS_KEY" != "$EXP_KEY" ]]; then
-          echo "Mismatched keys in results files - were these sorted properly?"
-          exit 1
-        fi
+        gcloud storage cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta*' ${REFERENCES}
 
-        if [[ "$OBS_KEY" == "call.step.event_key" ]]; then
-          # Skip the header
-          continue;
-        fi
+        # Temurin Java 8
+        apt-get -qq install wget apt-transport-https gnupg
+        wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | apt-key add -
+        echo "deb https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
+        apt-get -qq update
+        apt -qq install -y temurin-8-jdk
 
-        OBS_BYTES=${OBS[3]}
-        EXP_BYTES=${EXP[3]}
+        pip install ~{hail_wheel}
+        export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
 
-        TOLERANCE=0
+        export WORK=$PWD/work
+        mkdir ${WORK}
+        export AVRO=$PWD/avro
+        python3 ./hail_gvs_import.py --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
 
-        # For these two costs, there is non-determinism in the pipeline - we allow a % difference
-        if [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.BigQuery Query Scanned" ]]; then
-          TOLERANCE=0.015   # 1.5% tolerance  (Note - have seen as high as: 0.0109429)
-        elif [[ $OBS_KEY == "ExtractTask.GvsCreateCallset.Storage API Scanned" ]]; then
-          TOLERANCE=0.01   # 1% tolerance  (Note - have seen as high as: 0.00608656)
-        elif [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.Storage API Scanned" ]]; then
-          TOLERANCE=0.05  # 5% tolerance (Note - have seen as high as: 0.0281223)
-        fi
+        export LOCAL_VDS_PATH=${WORK}/gvs_export.vds
+        export JOINED_MATRIX_TABLE_PATH=${WORK}/joined.mt
 
-        if [[ $OBS_BYTES -ne $EXP_BYTES ]]; then
-          echo "The bytes observed ($OBS_BYTES) for '$OBS_KEY' differ from those expected ($EXP_BYTES)"
+        python3 ./hail_join_vds_vcfs.py --vds-path ${LOCAL_VDS_PATH} --joined-matrix-table-path ${JOINED_MATRIX_TABLE_PATH} *.vcf.gz
 
-          if [[ $OBS_BYTES -ge $EXP_BYTES ]]; then
-            DIFF_FOUND=$(echo $OBS_BYTES $EXP_BYTES | awk '{print ($1-$2)/$1}')
-          else
-            DIFF_FOUND=$(echo $EXP_BYTES $OBS_BYTES | awk '{print ($1-$2)/$1}')
-          fi
-
-          if ! awk "BEGIN{ exit ($DIFF_FOUND > $TOLERANCE) }"
-          then
-            echo "FAIL!!! The relative difference between these is $DIFF_FOUND, which is greater than the allowed tolerance ($TOLERANCE)"
-            echo "1" > ret_val.txt
-          else
-            echo "However, the relative difference between these is $DIFF_FOUND, which is below the allowed tolerance ($TOLERANCE)"
-          fi
-        fi
-        done
-
-        RET_VAL=`cat ret_val.txt`
-        exit $RET_VAL
+        # Copy up the VDS
+        gcloud storage cp --recursive ${LOCAL_VDS_PATH} ~{vds_destination_path}
 
+        pip install pytest
+        ln -s ${WORK}/joined.mt .
+        pytest ./gvs_vds_tie_out.py
     >>>
-
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
-        disks: "local-disk 10 HDD"
+        # `slim` here to be able to use Java
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-slim"
+        disks: "local-disk 2000 HDD"
+        memory: "30 GiB"
     }
-
     output {
-        File cost_observability_output_csv = "cost_observability_output.csv"
-    }
-}
-
-task AssertTableSizesAreExpected {
-    meta {
-        # we want to check the database each time this runs
-        volatile: true
-    }
-
-    input {
-        Boolean go = true
-        String dataset_name
-        String project_id
-        File expected_output_csv
-    }
-
-    command <<<
-        set -o errexit
-        set -o nounset
-        set -o pipefail
-
-        echo "project_id = ~{project_id}" > ~/.bigqueryrc
-        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
-            "SELECT 'vet_total' AS total_name, sum(total_billable_bytes) AS total_bytes FROM \
-            \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` WHERE table_name LIKE 'vet_%' \
-            UNION ALL \
-            SELECT 'ref_ranges_total' AS total_name, sum(total_billable_bytes) AS total_bytes \
-            FROM \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` \
-            WHERE table_name LIKE 'ref_ranges_%' ORDER BY total_name" > table_size_output.csv
-
-        set +o errexit
-        diff -w table_size_output.csv ~{expected_output_csv} > differences.txt
-        set -o errexit
-
-        if [[ -s differences.txt ]]; then
-            echo "Differences found:"
-            cat differences.txt
-            exit 1
-        fi
-    >>>
-
-    runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
-        disks: "local-disk 10 HDD"
-    }
-
-    output {
-        File table_size_output_csv = "table_size_output.csv"
-        File differences = "differences.txt"
+        Boolean done = true
     }
 }
diff --git a/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
index f0559e3523b..ce0cd2a7966 100644
--- a/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
@@ -104,6 +104,8 @@ workflow GvsQuickstartIntegration {
         Array[File] output_vcf_indexes = GvsUnified.output_vcf_indexes
         Float total_vcfs_size_mb = GvsUnified.total_vcfs_size_mb
         File manifest = GvsUnified.manifest
+        String dataset_name = BuildGATKJarAndCreateDataset.dataset_name
+        String filter_set_name = "quickit"
         Boolean done = true
     }
 }
diff --git a/scripts/variantstore/wdl/GvsUnifiedHail.wdl b/scripts/variantstore/wdl/GvsUnifiedHail.wdl
deleted file mode 100644
index ff800649f93..00000000000
--- a/scripts/variantstore/wdl/GvsUnifiedHail.wdl
+++ /dev/null
@@ -1,284 +0,0 @@
-version 1.0
-
-import "GvsAssignIds.wdl" as AssignIds
-import "GvsImportGenomes.wdl" as ImportGenomes
-import "GvsPopulateAltAllele.wdl" as PopulateAltAllele
-import "GvsCreateFilterSet.wdl" as CreateFilterSet
-import "GvsPrepareRangesCallset.wdl" as PrepareRangesCallset
-import "GvsExtractCallset.wdl" as ExtractCallset
-import "GvsExtractAvroFilesForHail.wdl" as ExtractAvroFilesForHail
-
-workflow GvsUnifiedHail {
-    input {
-        # Begin GvsAssignIds
-        String dataset_name
-        String project_id
-        String branch_name
-        String call_set_identifier = branch_name
-
-        Array[String] external_sample_names
-
-        File? gatk_override
-        # End GvsAssignIds
-
-        # Begin GvsImportGenomes
-        Array[File] input_vcfs
-        Array[File] input_vcf_indexes
-        File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
-
-        # set to "NONE" to ingest all the reference data into GVS for VDS (instead of VCF) output
-        String drop_state = "NONE"
-
-        # The larger the `load_data_batch_size` the greater the probability of preemptions and non-retryable
-        # BigQuery errors so if specifying this adjust preemptible and maxretries accordingly. Or just take the defaults,
-        # those should work fine in most cases.
-        Int? load_data_batch_size
-        Int? load_data_preemptible_override
-        Int? load_data_maxretries_override
-        # End GvsImportGenomes
-
-        # Begin GvsCreateFilterSet
-        String filter_set_name = call_set_identifier
-        Array[String] indel_recalibration_annotation_values = ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"]
-        Array[String] snp_recalibration_annotation_values = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"]
-
-        Int? INDEL_VQSR_max_gaussians_override = 4
-        Int? INDEL_VQSR_mem_gb_override
-        Int? SNP_VQSR_max_gaussians_override = 6
-        Int? SNP_VQSR_mem_gb_override
-        # End GvsCreateFilterSet
-
-        # Begin GvsPrepareRangesCallset
-        String extract_table_prefix
-
-        String query_project = project_id
-        String destination_project = project_id
-        String destination_dataset = dataset_name
-        String fq_temp_table_dataset = "~{destination_project}.~{destination_dataset}"
-
-        Array[String]? query_labels
-        File? sample_names_to_extract
-        # End GvsPrepareRangesCallset
-
-        # Begin GvsExtractCallset
-        Int? extract_scatter_count
-
-        File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
-
-        String extract_output_file_base_name = sub(filter_set_name, " ", "-")
-
-        Int? extract_maxretries_override
-        Int? extract_preemptible_override
-        String? extract_output_gcs_dir
-        Int? split_intervals_disk_size_override
-        Int? split_intervals_mem_override
-        Boolean extract_do_not_filter_override = false
-        # End GvsExtractCallset
-
-        # Begin CreateVds
-        File hail_wheel = "gs://gvs-internal-scratch/hail-wheels/2022-10-18/0.2.102-964bee061eb0/hail-0.2.102-py3-none-any.whl"
-        # End CreateVds
-    }
-
-    call AssignIds.GvsAssignIds as AssignIds {
-        input:
-            dataset_name = dataset_name,
-            project_id = project_id,
-            external_sample_names = external_sample_names,
-            assign_ids_gatk_override = gatk_override
-    }
-
-    call ImportGenomes.GvsImportGenomes {
-        input:
-            go = AssignIds.done,
-            dataset_name = dataset_name,
-            project_id = project_id,
-            external_sample_names = external_sample_names,
-            input_vcfs = input_vcfs,
-            input_vcf_indexes = input_vcf_indexes,
-            interval_list = interval_list,
-            load_data_preemptible_override = load_data_preemptible_override,
-            load_data_maxretries_override = load_data_maxretries_override,
-            load_data_gatk_override = gatk_override,
-            load_data_batch_size = load_data_batch_size,
-            drop_state = drop_state
-    }
-
-    call PopulateAltAllele.GvsPopulateAltAllele {
-        input:
-            call_set_identifier = call_set_identifier,
-            go = GvsImportGenomes.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,
-            indel_recalibration_annotation_values = indel_recalibration_annotation_values,
-            snp_recalibration_annotation_values = snp_recalibration_annotation_values,
-            interval_list = interval_list,
-            gatk_override = gatk_override,
-            INDEL_VQSR_max_gaussians_override = INDEL_VQSR_max_gaussians_override,
-            INDEL_VQSR_mem_gb_override = INDEL_VQSR_mem_gb_override,
-            SNP_VQSR_max_gaussians_override = SNP_VQSR_max_gaussians_override,
-            SNP_VQSR_mem_gb_override = SNP_VQSR_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
-    }
-
-    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
-        input:
-            go = GvsCreateFilterSet.done,
-            project_id = project_id,
-            dataset = dataset_name,
-            filter_set_name = filter_set_name,
-            scatter_width = 10,
-    }
-
-    call CreateVds {
-        input:
-            branch_name = branch_name,
-            hail_wheel = hail_wheel,
-            avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
-            vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
-            tieout_vcfs = GvsExtractCallset.output_vcfs,
-            tieout_vcf_indexes = GvsExtractCallset.output_vcf_indexes,
-    }
-
-    output {
-        Boolean done = true
-        Array[File] output_vcfs = GvsExtractCallset.output_vcfs
-        Array[File] output_vcf_indexes = GvsExtractCallset.output_vcf_indexes
-        Float total_vcfs_size_mb = GvsExtractCallset.total_vcfs_size_mb
-        Array[File] output_vcf_interval_files = GvsExtractCallset.output_vcf_interval_files
-        File? sample_name_list = GvsExtractCallset.sample_name_list
-        File manifest = GvsExtractCallset.manifest
-        String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
-    }
-}
-
-task CreateVds {
-    input {
-        File hail_wheel
-        String branch_name
-        String avro_prefix
-        String vds_destination_path
-        Array[File] tieout_vcfs
-        Array[File] tieout_vcf_indexes
-    }
-    parameter_meta {
-        tieout_vcfs: {
-            localization_optional: true
-        }
-        tieout_vcf_indexes: {
-            localization_optional: true
-        }
-    }
-    command <<<
-        # Prepend date, time and pwd to xtrace log entries.
-        PS4='\D{+%F %T} \w $ '
-        set -o errexit -o nounset -o pipefail -o xtrace
-
-        script_url_prefix="https://raw.githubusercontent.com/broadinstitute/gatk/~{branch_name}/scripts/variantstore/wdl/extract"
-
-        for script in hail_gvs_import.py hail_join_vds_vcfs.py gvs_vds_tie_out.py
-        do
-            curl --silent --location --remote-name "${script_url_prefix}/${script}"
-        done
-
-        # Create a manifest of VCFs and indexes to bulk download with `gcloud storage cp`.
-        touch vcf_manifest.txt
-        for file in ~{sep=' ' tieout_vcfs} ~{sep=' ' tieout_vcf_indexes}
-        do
-            echo $file >> vcf_manifest.txt
-        done
-
-        # Copy VCFs and indexes to the current directory.
-        cat vcf_manifest.txt | gcloud storage cp -I .
-
-        # `avro_prefix` includes a trailing `avro` so don't add another `avro` here.
-        gcloud storage cp --recursive ~{avro_prefix} $PWD
-
-        export REFERENCES=$PWD/references
-        mkdir -p ${REFERENCES}
-
-        gcloud storage cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta*' ${REFERENCES}
-
-        # Temurin Java 8
-        apt-get -qq install wget apt-transport-https gnupg
-        wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | apt-key add -
-        echo "deb https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
-        apt-get -qq update
-        apt -qq install -y temurin-8-jdk
-
-        pip install ~{hail_wheel}
-        export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
-
-        export WORK=$PWD/work
-        mkdir ${WORK}
-        export AVRO=$PWD/avro
-        python3 ./hail_gvs_import.py --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
-
-        export LOCAL_VDS_PATH=${WORK}/gvs_export.vds
-        export JOINED_MATRIX_TABLE_PATH=${WORK}/joined.mt
-
-        python3 ./hail_join_vds_vcfs.py --vds-path ${LOCAL_VDS_PATH} --joined-matrix-table-path ${JOINED_MATRIX_TABLE_PATH} *.vcf.gz
-
-        # Copy up the VDS
-        gcloud storage cp --recursive ${LOCAL_VDS_PATH} ~{vds_destination_path}
-
-        pip install pytest
-        ln -s ${WORK}/joined.mt .
-        pytest ./gvs_vds_tie_out.py
-    >>>
-    runtime {
-        # `slim` here to be able to use Java
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-slim"
-        disks: "local-disk 2000 HDD"
-        memory: "30 GiB"
-    }
-    output {
-        Boolean done = true
-    }
-}

From d207592cce92b251a9954def6e2ce89eed982375 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 15:07:15 -0400
Subject: [PATCH 22/49] restore my beauteous whitespace

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 9d226a7e842..f01277ecb2c 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -73,14 +73,14 @@ task CreateVds {
 
         for script in hail_gvs_import.py hail_join_vds_vcfs.py gvs_vds_tie_out.py
         do
-        curl --silent --location --remote-name "${script_url_prefix}/${script}"
+            curl --silent --location --remote-name "${script_url_prefix}/${script}"
         done
 
         # Create a manifest of VCFs and indexes to bulk download with `gcloud storage cp`.
         touch vcf_manifest.txt
         for file in ~{sep=' ' tieout_vcfs} ~{sep=' ' tieout_vcf_indexes}
         do
-        echo $file >> vcf_manifest.txt
+            echo $file >> vcf_manifest.txt
         done
 
         # Copy VCFs and indexes to the current directory.

From c751af31b289f4faa76a2357c07807cda80b28f4 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 15:09:54 -0400
Subject: [PATCH 23/49] oops need drop_state NONE

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index f01277ecb2c..5647216e1c2 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -15,6 +15,7 @@ workflow GvsQuickstartHailIntegration {
     call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
         input:
             branch_name = branch_name,
+            drop_state = "NONE",
     }
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {

From 99e867c613bf8369ce1ff43f1cb5bf9e0c964758 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 27 Oct 2022 19:20:46 -0400
Subject: [PATCH 24/49] hackery for short cycle times

---
 .../wdl/GvsQuickstartHailIntegration.wdl      | 259 +++++++++++++++++-
 1 file changed, 245 insertions(+), 14 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 5647216e1c2..8bf6545544a 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -12,36 +12,267 @@ workflow GvsQuickstartHailIntegration {
 
     String project_id = "gvs-internal"
 
-    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
-        input:
-            branch_name = branch_name,
-            drop_state = "NONE",
-    }
+#    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
+#        input:
+#            branch_name = branch_name,
+#            drop_state = "NONE",
+#    }
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
         input:
-            go = QuickstartVCFIntegration.done,
             project_id = project_id,
-            dataset = QuickstartVCFIntegration.dataset_name,
-            filter_set_name = QuickstartVCFIntegration.filter_set_name,
+            dataset = "quickit_vs_639_hail_testing_spike_491d938",
+            filter_set_name = "quickit",
             scatter_width = 10,
     }
 
+    Array[File] output_vcfs = [
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-14/0000000014-quickit.vcf.gz",
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+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz",
+                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz"
+                              ]
+
+
+    Array[File] output_vcf_indexes = [
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-14/0000000014-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-15/0000000015-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-16/0000000016-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-17/0000000017-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-18/0000000018-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-19/0000000019-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-20/0000000020-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-21/0000000021-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-22/0000000022-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-23/0000000023-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-24/0000000024-quickit.vcf.gz.tbi",
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+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-87/0000000087-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-88/0000000088-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-89/0000000089-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-90/0000000090-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-91/0000000091-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-92/0000000092-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-93/0000000093-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-94/0000000094-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-95/0000000095-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-96/0000000096-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-97/0000000097-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-98/0000000098-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-99/0000000099-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-100/0000000100-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz.tbi",
+                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz.tbi"
+                                     ]
+
+
     call CreateVds {
         input:
             branch_name = branch_name,
             hail_wheel = hail_wheel,
             avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
             vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
-            tieout_vcfs = QuickstartVCFIntegration.output_vcfs,
-            tieout_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes,
+            tieout_vcfs = output_vcfs,
+            tieout_vcf_indexes = output_vcf_indexes,
     }
 
     output {
-        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
-        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
-        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
-        File manifest = QuickstartVCFIntegration.manifest
+#        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
+#        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
+#        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
+#        File manifest = QuickstartVCFIntegration.manifest
         String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
         Boolean done = true
     }

From 1210bb276f81665e1afaa0ff46d728feb771794c Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Fri, 28 Oct 2022 13:14:16 -0400
Subject: [PATCH 25/49] Revert "hackery for short cycle times"

This reverts commit 74f9be71b91e994a89a66db05032961e0e0c8d8b.
---
 .../wdl/GvsQuickstartHailIntegration.wdl      | 259 +-----------------
 1 file changed, 14 insertions(+), 245 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 8bf6545544a..5647216e1c2 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -12,267 +12,36 @@ workflow GvsQuickstartHailIntegration {
 
     String project_id = "gvs-internal"
 
-#    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
-#        input:
-#            branch_name = branch_name,
-#            drop_state = "NONE",
-#    }
+    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
+        input:
+            branch_name = branch_name,
+            drop_state = "NONE",
+    }
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
         input:
+            go = QuickstartVCFIntegration.done,
             project_id = project_id,
-            dataset = "quickit_vs_639_hail_testing_spike_491d938",
-            filter_set_name = "quickit",
+            dataset = QuickstartVCFIntegration.dataset_name,
+            filter_set_name = QuickstartVCFIntegration.filter_set_name,
             scatter_width = 10,
     }
 
-    Array[File] output_vcfs = [
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz",
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-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-97/0000000097-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-98/0000000098-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-99/0000000099-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-100/0000000100-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz",
-                              "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz"
-                              ]
-
-
-    Array[File] output_vcf_indexes = [
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz.tbi",
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-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz.tbi",
-                                     "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/78da4fb5-9074-4634-9c53-84682b2ec3ec/GvsQuickstartHailIntegration/26aee20f-cff2-433c-97e8-6aa55f9f77aa/call-QuickstartVCFIntegration/GvsQuickstartIntegration/6200a03f-015b-4bfd-a786-6aa799c4e6b9/call-GvsUnified/GvsUnified/d74457c7-4742-41a8-9710-33a9cea9d5ee/call-GvsExtractCallset/GvsExtractCallset/e57be981-b23f-4c0d-b56b-60cbe6b7fcfb/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz.tbi"
-                                     ]
-
-
     call CreateVds {
         input:
             branch_name = branch_name,
             hail_wheel = hail_wheel,
             avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
             vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
-            tieout_vcfs = output_vcfs,
-            tieout_vcf_indexes = output_vcf_indexes,
+            tieout_vcfs = QuickstartVCFIntegration.output_vcfs,
+            tieout_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes,
     }
 
     output {
-#        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
-#        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
-#        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
-#        File manifest = QuickstartVCFIntegration.manifest
+        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
+        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
+        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
+        File manifest = QuickstartVCFIntegration.manifest
         String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
         Boolean done = true
     }

From 3b0ec84fd3612ffe695b91255851302c57508da3 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Fri, 28 Oct 2022 14:31:30 -0400
Subject: [PATCH 26/49] fixees

---
 .../wdl/GvsQuickstartHailIntegration.wdl      |  1 +
 .../wdl/GvsQuickstartIntegration.wdl          | 46 ++++++++++---------
 2 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 5647216e1c2..e24bbe6b915 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -16,6 +16,7 @@ workflow GvsQuickstartHailIntegration {
         input:
             branch_name = branch_name,
             drop_state = "NONE",
+            extract_do_not_filter_override = false,
     }
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
diff --git a/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
index ce0cd2a7966..ded696ec828 100644
--- a/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
@@ -50,6 +50,7 @@ workflow GvsQuickstartIntegration {
 
         Int? extract_scatter_count
         String drop_state = "FORTY"
+        Boolean extract_do_not_filter_override = true
     }
     String project_id = "gvs-internal"
 
@@ -73,30 +74,33 @@ workflow GvsQuickstartIntegration {
             extract_scatter_count = extract_scatter_count,
             # Force filtering off as it is not deterministic and the initial version of this integration test does not
             # allow for inexact matching of actual and expected results.
-            extract_do_not_filter_override = true,
+            extract_do_not_filter_override = extract_do_not_filter_override,
             drop_state = drop_state
     }
 
-    call AssertIdenticalOutputs {
-        input:
-            expected_output_prefix = expected_output_prefix,
-            actual_vcfs = GvsUnified.output_vcfs
-    }
-
-    call AssertCostIsTrackedAndExpected {
-        input:
-            go = GvsUnified.done,
-            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-            project_id = project_id,
-            expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
-    }
-
-    call AssertTableSizesAreExpected {
-        input:
-            go = GvsUnified.done,
-            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-            project_id = project_id,
-            expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
+    # Only assert identical outputs if we did not filter (filtering is not deterministic)
+    if (extract_do_not_filter_override) {
+        call AssertIdenticalOutputs {
+            input:
+                expected_output_prefix = expected_output_prefix,
+                actual_vcfs = GvsUnified.output_vcfs
+        }
+
+        call AssertCostIsTrackedAndExpected {
+            input:
+                go = GvsUnified.done,
+                dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+                project_id = project_id,
+                expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
+        }
+
+        call AssertTableSizesAreExpected {
+            input:
+                go = GvsUnified.done,
+                dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+                project_id = project_id,
+                expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
+        }
     }
 
     output {

From 54c06c8d0bf05459a986cccde31d3ac389ef01fc Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Wed, 2 Nov 2022 11:00:39 -0400
Subject: [PATCH 27/49] wip

---
 .../wdl/GvsQuickstartHailIntegration.wdl            |  8 ++++++--
 scripts/variantstore/wdl/extract/gvs_vds_tie_out.py | 13 -------------
 2 files changed, 6 insertions(+), 15 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index e24bbe6b915..3f64befb735 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -28,7 +28,7 @@ workflow GvsQuickstartHailIntegration {
             scatter_width = 10,
     }
 
-    call CreateVds {
+    call CreateAndTieOutVds {
         input:
             branch_name = branch_name,
             hail_wheel = hail_wheel,
@@ -49,7 +49,7 @@ workflow GvsQuickstartHailIntegration {
 }
 
 
-task CreateVds {
+task CreateAndTieOutVds {
     input {
         File hail_wheel
         String branch_name
@@ -80,10 +80,14 @@ task CreateVds {
 
         # Create a manifest of VCFs and indexes to bulk download with `gcloud storage cp`.
         touch vcf_manifest.txt
+        # This is extremely noisy and not interesting, turn off xtrace.
+        set +o xtrace
         for file in ~{sep=' ' tieout_vcfs} ~{sep=' ' tieout_vcf_indexes}
         do
             echo $file >> vcf_manifest.txt
         done
+        # xtrace back on
+        set -o xtrace
 
         # Copy VCFs and indexes to the current directory.
         cat vcf_manifest.txt | gcloud storage cp -I .
diff --git a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
index 6ff70b1dc53..4bc774a38a3 100644
--- a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
+++ b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
@@ -122,7 +122,6 @@ def find_violations(ht, predicate):
     if violations > 0:
         ht = ht.filter(~ht.CHECK)
         ht.show()
-
         assert False, f'{violations} violations'
 
 
@@ -174,18 +173,6 @@ def test_ft_equivalence():
                     .default(False))
 
 
-def test_call_stats_equivalence():
-    mt = updated_local_alleles(ft_filter(gq0_filter()))
-    mt = mt.annotate_rows(
-        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
-                                         hl.len(mt.vds_row.alleles)))
-    r = mt.rows()
-    find_violations(r, (r.vds_call_stats.AN == r.vcf_row.info.AN)
-                    & hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF,
-                                                       f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01)))
-                    & ((r.vds_call_stats.AC[1:] == r.vcf_row.info.AC)))
-
-
 def test_call_stats_equivalence_an():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
     mt = mt.annotate_rows(

From 2926093e2f4fa85a5bd5678b62acab0f0d7bd511 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Wed, 2 Nov 2022 14:41:19 -0400
Subject: [PATCH 28/49] wip

---
 .../variantstore/wdl/extract/gvs_vds_tie_out.py    | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
index 4bc774a38a3..d52bcbffb0b 100644
--- a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
+++ b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
@@ -72,6 +72,7 @@
     }
     'vds_entry': struct {
         LGT: call,
+        GT: call,
         GQ: int32,
         RGQ: int32,
         LAD: array<int32>,
@@ -97,14 +98,14 @@ def updated_local_alleles(mt=mt):
 def gq0_filter(mt=mt):
     """Sets VDS LGTs to missing at reference genotypes when GQ is 0"""
     mt2 = mt.annotate_entries(vds_entry=mt.vds_entry.annotate(
-        LGT=hl.or_missing(mt.vds_entry.LGT.is_non_ref() | (mt.vds_entry.GQ > 0), mt.vds_entry.LGT)))
+        GT=hl.or_missing(mt.vds_entry.GT.is_non_ref() | (mt.vds_entry.GQ > 0), mt.vds_entry.GT)))
     return mt2
 
 
 def ft_filter(mt=mt):
     """Sets VDS LGTs to missing at non-ref genotypes when FT is False"""
     mt2 = mt.annotate_entries(
-        vds_entry=mt.vds_entry.annotate(LGT=hl.or_missing(hl.coalesce(mt.vds_entry.FT, True), mt.vds_entry.LGT)))
+        vds_entry=mt.vds_entry.annotate(GT=hl.or_missing(hl.coalesce(mt.vds_entry.FT, True), mt.vds_entry.GT)))
     return mt2
 
 
@@ -176,8 +177,7 @@ def test_ft_equivalence():
 def test_call_stats_equivalence_an():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
     mt = mt.annotate_rows(
-        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
-                                         hl.len(mt.vds_row.alleles)))
+        vds_call_stats=hl.agg.call_stats(mt.vds_entry.GT, hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, (r.vds_call_stats.AN == r.vcf_row.info.AN))
 
@@ -185,8 +185,7 @@ def test_call_stats_equivalence_an():
 def test_call_stats_equivalence_ac():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
     mt = mt.annotate_rows(
-        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
-                                         hl.len(mt.vds_row.alleles)))
+        vds_call_stats=hl.agg.call_stats(mt.vds_entry.GT, hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, (r.vds_call_stats.AC[1:] == r.vcf_row.info.AC))
 
@@ -194,8 +193,7 @@ def test_call_stats_equivalence_ac():
 def test_call_stats_equivalence_af():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
     mt = mt.annotate_rows(
-        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
-                                         hl.len(mt.vds_row.alleles)))
+        vds_call_stats=hl.agg.call_stats(mt.vds_entry.GT, hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF,
                                                         f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01))))

From 397268f38b1f0a2bc4a3b37638e702b625c58233 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Wed, 2 Nov 2022 15:21:27 -0400
Subject: [PATCH 29/49] fix from Tim

---
 scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
index 6b62b046cbc..a6eae89971a 100644
--- a/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
+++ b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
@@ -4,9 +4,11 @@
 
 def vds_mt(vds_path):
     vds = hl.vds.read_vds(vds_path)
+    # Currently required as otherwise GT takes priority but AC will be wrong as alleles will be mistmatched
+    vds.variant_data = vds.variant_data.drop('GT')
     mt = hl.vds.to_dense_mt(vds)
-    vds_path = 'vds_dense.mt'
-    mt.write(vds_path, overwrite=True)
+    dense_vds_path = 'vds_dense.mt'
+    mt.write(dense_vds_path, overwrite=True)
     mt = hl.read_matrix_table(vds_path).key_rows_by('locus')
     return mt
 

From 0b0b84aee10202154700d904f7fbe03ad34bb3ee Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Wed, 2 Nov 2022 15:22:18 -0400
Subject: [PATCH 30/49] Revert "wip"

This reverts commit 591b57234bcdb05e3fe4a60430ef5d6992a8dda0.
---
 .../variantstore/wdl/extract/gvs_vds_tie_out.py    | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
index d52bcbffb0b..4bc774a38a3 100644
--- a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
+++ b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
@@ -72,7 +72,6 @@
     }
     'vds_entry': struct {
         LGT: call,
-        GT: call,
         GQ: int32,
         RGQ: int32,
         LAD: array<int32>,
@@ -98,14 +97,14 @@ def updated_local_alleles(mt=mt):
 def gq0_filter(mt=mt):
     """Sets VDS LGTs to missing at reference genotypes when GQ is 0"""
     mt2 = mt.annotate_entries(vds_entry=mt.vds_entry.annotate(
-        GT=hl.or_missing(mt.vds_entry.GT.is_non_ref() | (mt.vds_entry.GQ > 0), mt.vds_entry.GT)))
+        LGT=hl.or_missing(mt.vds_entry.LGT.is_non_ref() | (mt.vds_entry.GQ > 0), mt.vds_entry.LGT)))
     return mt2
 
 
 def ft_filter(mt=mt):
     """Sets VDS LGTs to missing at non-ref genotypes when FT is False"""
     mt2 = mt.annotate_entries(
-        vds_entry=mt.vds_entry.annotate(GT=hl.or_missing(hl.coalesce(mt.vds_entry.FT, True), mt.vds_entry.GT)))
+        vds_entry=mt.vds_entry.annotate(LGT=hl.or_missing(hl.coalesce(mt.vds_entry.FT, True), mt.vds_entry.LGT)))
     return mt2
 
 
@@ -177,7 +176,8 @@ def test_ft_equivalence():
 def test_call_stats_equivalence_an():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
     mt = mt.annotate_rows(
-        vds_call_stats=hl.agg.call_stats(mt.vds_entry.GT, hl.len(mt.vds_row.alleles)))
+        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
+                                         hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, (r.vds_call_stats.AN == r.vcf_row.info.AN))
 
@@ -185,7 +185,8 @@ def test_call_stats_equivalence_an():
 def test_call_stats_equivalence_ac():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
     mt = mt.annotate_rows(
-        vds_call_stats=hl.agg.call_stats(mt.vds_entry.GT, hl.len(mt.vds_row.alleles)))
+        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
+                                         hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, (r.vds_call_stats.AC[1:] == r.vcf_row.info.AC))
 
@@ -193,7 +194,8 @@ def test_call_stats_equivalence_ac():
 def test_call_stats_equivalence_af():
     mt = updated_local_alleles(ft_filter(gq0_filter()))
     mt = mt.annotate_rows(
-        vds_call_stats=hl.agg.call_stats(mt.vds_entry.GT, hl.len(mt.vds_row.alleles)))
+        vds_call_stats=hl.agg.call_stats(hl.vds.lgt_to_gt(mt.vds_entry.LGT, hl.coalesce(mt.vds_entry.LA_vcf, [0])),
+                                         hl.len(mt.vds_row.alleles)))
     r = mt.rows()
     find_violations(r, hl.all(lambda x: x, hl._zip_func(r.vds_call_stats.AF[1:], r.vcf_row.info.AF,
                                                         f=lambda t1, t2: hl.approx_equal(t1, t2, tolerance=0.01))))

From e3fb81fa30365ff276a67f385f89a01cf5312326 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 04:51:27 -0400
Subject: [PATCH 31/49] hacked up to resume

---
 .../wdl/GvsQuickstartHailIntegration.wdl      | 280 ++++++++++++++++--
 1 file changed, 257 insertions(+), 23 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 3f64befb735..bca7645ceb7 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -12,38 +12,272 @@ workflow GvsQuickstartHailIntegration {
 
     String project_id = "gvs-internal"
 
-    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
-        input:
-            branch_name = branch_name,
-            drop_state = "NONE",
-            extract_do_not_filter_override = false,
-    }
+#    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
+#        input:
+#            branch_name = branch_name,
+#            drop_state = "NONE",
+#            extract_do_not_filter_override = false,
+#    }
+#
+#    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
+#        input:
+#            go = QuickstartVCFIntegration.done,
+#            project_id = project_id,
+#            dataset = QuickstartVCFIntegration.dataset_name,
+#            filter_set_name = QuickstartVCFIntegration.filter_set_name,
+#            scatter_width = 10,
+#    }
 
-    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
-        input:
-            go = QuickstartVCFIntegration.done,
-            project_id = project_id,
-            dataset = QuickstartVCFIntegration.dataset_name,
-            filter_set_name = QuickstartVCFIntegration.filter_set_name,
-            scatter_width = 10,
-    }
+    String avro_prefix = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/1d9f3015-4c9e-4948-b837-975c2b9d029a/call-OutputPath/avro"
+
+    String vds_path = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/1d9f3015-4c9e-4948-b837-975c2b9d029a/call-OutputPath/2022-11-02-4c71c1ad/gvs_export.vds"
+
+    Array[File] output_vcfs = [
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-14/0000000014-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-15/0000000015-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-16/0000000016-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-17/0000000017-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-18/0000000018-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-19/0000000019-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-20/0000000020-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-21/0000000021-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-22/0000000022-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-23/0000000023-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-24/0000000024-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-25/0000000025-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-26/0000000026-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-27/0000000027-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-28/0000000028-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-29/0000000029-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-30/0000000030-quickit.vcf.gz",
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+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-99/0000000099-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-100/0000000100-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz"
+]
+
+    Array[File] output_vcf_indexes = [
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-14/0000000014-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-15/0000000015-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-16/0000000016-quickit.vcf.gz.tbi",
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+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-83/0000000083-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-84/0000000084-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-85/0000000085-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-86/0000000086-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-87/0000000087-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-88/0000000088-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-89/0000000089-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-90/0000000090-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-91/0000000091-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-92/0000000092-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-93/0000000093-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-94/0000000094-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-95/0000000095-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-96/0000000096-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-97/0000000097-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-98/0000000098-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-99/0000000099-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-100/0000000100-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz.tbi",
+  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz.tbi"
+]
 
     call CreateAndTieOutVds {
         input:
             branch_name = branch_name,
             hail_wheel = hail_wheel,
-            avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
-            vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
-            tieout_vcfs = QuickstartVCFIntegration.output_vcfs,
-            tieout_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes,
+            avro_prefix = avro_prefix,
+            vds_destination_path = vds_path,
+            tieout_vcfs = output_vcfs,
+            tieout_vcf_indexes = output_vcf_indexes,
     }
 
     output {
-        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
-        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
-        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
-        File manifest = QuickstartVCFIntegration.manifest
-        String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
+        #Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
+        #Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
+        #Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
+        #File manifest = QuickstartVCFIntegration.manifest
+        #String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
         Boolean done = true
     }
 }

From b1d5dad91a0defd0f6e9deab3c30eb390389b3e7 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 05:49:09 -0400
Subject: [PATCH 32/49] whoops

---
 scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
index a6eae89971a..4ddb0d9d8b9 100644
--- a/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
+++ b/scripts/variantstore/wdl/extract/hail_join_vds_vcfs.py
@@ -4,12 +4,13 @@
 
 def vds_mt(vds_path):
     vds = hl.vds.read_vds(vds_path)
-    # Currently required as otherwise GT takes priority but AC will be wrong as alleles will be mistmatched
+    # This is currently required as otherwise GT takes priority but AC will be wrong as alleles will be in different
+    # orders in the VCF versus VDS representations.
     vds.variant_data = vds.variant_data.drop('GT')
     mt = hl.vds.to_dense_mt(vds)
     dense_vds_path = 'vds_dense.mt'
     mt.write(dense_vds_path, overwrite=True)
-    mt = hl.read_matrix_table(vds_path).key_rows_by('locus')
+    mt = hl.read_matrix_table(dense_vds_path).key_rows_by('locus')
     return mt
 
 

From 721cc2a38a575e6bacf5108f54adc3a8b096ed1f Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 07:17:21 -0400
Subject: [PATCH 33/49] Revert "hacked up to resume"

This reverts commit d03e345efb3e9ce43d4a70191396eab00b43e63c.
---
 .../wdl/GvsQuickstartHailIntegration.wdl      | 280 ++----------------
 1 file changed, 23 insertions(+), 257 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index bca7645ceb7..3f64befb735 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -12,272 +12,38 @@ workflow GvsQuickstartHailIntegration {
 
     String project_id = "gvs-internal"
 
-#    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
-#        input:
-#            branch_name = branch_name,
-#            drop_state = "NONE",
-#            extract_do_not_filter_override = false,
-#    }
-#
-#    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
-#        input:
-#            go = QuickstartVCFIntegration.done,
-#            project_id = project_id,
-#            dataset = QuickstartVCFIntegration.dataset_name,
-#            filter_set_name = QuickstartVCFIntegration.filter_set_name,
-#            scatter_width = 10,
-#    }
-
-    String avro_prefix = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/1d9f3015-4c9e-4948-b837-975c2b9d029a/call-OutputPath/avro"
-
-    String vds_path = "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-GvsExtractAvroFilesForHail/GvsExtractAvroFilesForHail/1d9f3015-4c9e-4948-b837-975c2b9d029a/call-OutputPath/2022-11-02-4c71c1ad/gvs_export.vds"
-
-    Array[File] output_vcfs = [
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-14/0000000014-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-15/0000000015-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-16/0000000016-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-17/0000000017-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-18/0000000018-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-19/0000000019-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-20/0000000020-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-21/0000000021-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-22/0000000022-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-23/0000000023-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-24/0000000024-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-25/0000000025-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-26/0000000026-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-27/0000000027-quickit.vcf.gz",
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-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-96/0000000096-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-97/0000000097-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-98/0000000098-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-99/0000000099-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-100/0000000100-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz"
-]
+    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
+        input:
+            branch_name = branch_name,
+            drop_state = "NONE",
+            extract_do_not_filter_override = false,
+    }
 
-    Array[File] output_vcf_indexes = [
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-0/0000000000-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-1/0000000001-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-2/0000000002-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-3/0000000003-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-4/0000000004-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-5/0000000005-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-6/0000000006-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-7/0000000007-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-8/0000000008-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-9/0000000009-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-10/0000000010-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-11/0000000011-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-12/0000000012-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-13/0000000013-quickit.vcf.gz.tbi",
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-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-80/0000000080-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-81/0000000081-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-82/0000000082-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-83/0000000083-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-84/0000000084-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-85/0000000085-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-86/0000000086-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-87/0000000087-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-88/0000000088-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-89/0000000089-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-90/0000000090-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-91/0000000091-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-92/0000000092-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-93/0000000093-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-94/0000000094-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-95/0000000095-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-96/0000000096-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-97/0000000097-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-98/0000000098-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-99/0000000099-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-100/0000000100-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-101/0000000101-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-102/0000000102-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-103/0000000103-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-104/0000000104-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-105/0000000105-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-106/0000000106-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-107/0000000107-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-108/0000000108-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-109/0000000109-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-110/0000000110-quickit.vcf.gz.tbi",
-  "gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/23160c97-d2c0-4292-85b0-e1835d31d3c6/GvsQuickstartHailIntegration/ce9c9d78-bcb7-463c-beb6-751d4f840e9b/call-QuickstartVCFIntegration/GvsQuickstartIntegration/649172b6-03ff-4084-b153-ea62675d5335/call-GvsUnified/GvsUnified/ba7b10b2-1ec7-4967-8880-02c31afbca43/call-GvsExtractCallset/GvsExtractCallset/54204852-b40e-4ee5-af27-b66c21e92a35/call-ExtractTask/shard-111/0000000111-quickit.vcf.gz.tbi"
-]
+    call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
+        input:
+            go = QuickstartVCFIntegration.done,
+            project_id = project_id,
+            dataset = QuickstartVCFIntegration.dataset_name,
+            filter_set_name = QuickstartVCFIntegration.filter_set_name,
+            scatter_width = 10,
+    }
 
     call CreateAndTieOutVds {
         input:
             branch_name = branch_name,
             hail_wheel = hail_wheel,
-            avro_prefix = avro_prefix,
-            vds_destination_path = vds_path,
-            tieout_vcfs = output_vcfs,
-            tieout_vcf_indexes = output_vcf_indexes,
+            avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
+            vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
+            tieout_vcfs = QuickstartVCFIntegration.output_vcfs,
+            tieout_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes,
     }
 
     output {
-        #Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
-        #Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
-        #Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
-        #File manifest = QuickstartVCFIntegration.manifest
-        #String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
+        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
+        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
+        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
+        File manifest = QuickstartVCFIntegration.manifest
+        String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
         Boolean done = true
     }
 }

From 29789310ca2b79f0acbc5d0cf037ba220d0d8f99 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 15:42:35 -0400
Subject: [PATCH 34/49] uber integration wdl

---
 .dockstore.yml                                |  12 +-
 .../wdl/GvsQuickstartHailIntegration.wdl      |  22 +-
 .../wdl/GvsQuickstartIntegration.wdl          | 349 +----------------
 .../wdl/GvsQuickstartVcfIntegration.wdl       | 351 ++++++++++++++++++
 .../extract/test_workflow_compute_costs.py    |   4 +-
 .../workflow_compute_costs_test_helper.py     |  12 +-
 6 files changed, 394 insertions(+), 356 deletions(-)
 create mode 100644 scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl

diff --git a/.dockstore.yml b/.dockstore.yml
index b1580b28f0b..cadda34c7a5 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -201,9 +201,9 @@ workflows:
        branches:
          - master
          - ah_var_store
-   - name: GvsQuickstartIntegration
+   - name: GvsQuickstartVcfIntegration
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
      filters:
        branches:
          - master
@@ -216,6 +216,14 @@ workflows:
          - master
          - ah_var_store
          - vs_639_hail_testing_spike
+   - name: GvsQuickstartIntegration
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - vs_639_hail_testing_spike
    - name: GvsIngestTieout
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 3f64befb735..c80d5eb135f 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -2,7 +2,7 @@ version 1.0
 
 import "GvsUtils.wdl" as Utils
 import "GvsExtractAvroFilesForHail.wdl" as ExtractAvroFilesForHail
-import "GvsQuickstartIntegration.wdl" as QuickstartVCFIntegration
+import "GvsQuickstartVcfIntegration.wdl" as QuickstartVcfIntegration
 
 workflow GvsQuickstartHailIntegration {
     input {
@@ -12,7 +12,7 @@ workflow GvsQuickstartHailIntegration {
 
     String project_id = "gvs-internal"
 
-    call QuickstartVCFIntegration.GvsQuickstartIntegration as QuickstartVCFIntegration {
+    call QuickstartVcfIntegration.GvsQuickstartVcfIntegration {
         input:
             branch_name = branch_name,
             drop_state = "NONE",
@@ -21,10 +21,10 @@ workflow GvsQuickstartHailIntegration {
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
         input:
-            go = QuickstartVCFIntegration.done,
+            go = GvsQuickstartVcfIntegration.done,
             project_id = project_id,
-            dataset = QuickstartVCFIntegration.dataset_name,
-            filter_set_name = QuickstartVCFIntegration.filter_set_name,
+            dataset = GvsQuickstartVcfIntegration.dataset_name,
+            filter_set_name = GvsQuickstartVcfIntegration.filter_set_name,
             scatter_width = 10,
     }
 
@@ -34,15 +34,15 @@ workflow GvsQuickstartHailIntegration {
             hail_wheel = hail_wheel,
             avro_prefix = GvsExtractAvroFilesForHail.avro_prefix,
             vds_destination_path = GvsExtractAvroFilesForHail.vds_output_path,
-            tieout_vcfs = QuickstartVCFIntegration.output_vcfs,
-            tieout_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes,
+            tieout_vcfs = GvsQuickstartVcfIntegration.output_vcfs,
+            tieout_vcf_indexes = GvsQuickstartVcfIntegration.output_vcf_indexes,
     }
 
     output {
-        Array[File] output_vcfs = QuickstartVCFIntegration.output_vcfs
-        Array[File] output_vcf_indexes = QuickstartVCFIntegration.output_vcf_indexes
-        Float total_vcfs_size_mb = QuickstartVCFIntegration.total_vcfs_size_mb
-        File manifest = QuickstartVCFIntegration.manifest
+        Array[File] output_vcfs = GvsQuickstartVcfIntegration.output_vcfs
+        Array[File] output_vcf_indexes = GvsQuickstartVcfIntegration.output_vcf_indexes
+        Float total_vcfs_size_mb = GvsQuickstartVcfIntegration.total_vcfs_size_mb
+        File manifest = GvsQuickstartVcfIntegration.manifest
         String vds_output_path = GvsExtractAvroFilesForHail.vds_output_path
         Boolean done = true
     }
diff --git a/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
index ded696ec828..2092e135a3c 100644
--- a/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
@@ -1,351 +1,30 @@
 version 1.0
 
-import "GvsUnified.wdl" as Unified
-import "GvsUtils.wdl" as Utils
+import "GvsQuickstartVcfIntegration.wdl" as QuickstartVcfIntegration
+import "GvsQuickstartHailIntegration.wdl" as QuickstartHailIntegration
 
 workflow GvsQuickstartIntegration {
-
     input {
         String branch_name
-        String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-10-20/"
-
-        Array[String] external_sample_names = [
-                                              "ERS4367795",
-                                              "ERS4367796",
-                                              "ERS4367797",
-                                              "ERS4367798",
-                                              "ERS4367799",
-                                              "ERS4367800",
-                                              "ERS4367801",
-                                              "ERS4367803",
-                                              "ERS4367804",
-                                              "ERS4367805"
-                                              ]
-
-        Array[File] input_vcfs = [
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
-                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz"
-                                 ]
-
-        Array[File] input_vcf_indexes = [
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
-                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi"
-                                        ]
-
-        Int? extract_scatter_count
-        String drop_state = "FORTY"
-        Boolean extract_do_not_filter_override = true
-    }
-    String project_id = "gvs-internal"
-
-    call Utils.BuildGATKJarAndCreateDataset {
-        input:
-            branch_name = branch_name,
-            dataset_prefix = "quickit"
-    }
-
-    call Unified.GvsUnified {
-        input:
-            call_set_identifier = branch_name,
-            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-            project_id = project_id,
-            external_sample_names = external_sample_names,
-            gatk_override = BuildGATKJarAndCreateDataset.jar,
-            input_vcfs = input_vcfs,
-            input_vcf_indexes = input_vcf_indexes,
-            filter_set_name = "quickit",
-            extract_table_prefix = "quickit",
-            extract_scatter_count = extract_scatter_count,
-            # Force filtering off as it is not deterministic and the initial version of this integration test does not
-            # allow for inexact matching of actual and expected results.
-            extract_do_not_filter_override = extract_do_not_filter_override,
-            drop_state = drop_state
+        Boolean run_vcf_integration = true
+        Boolean run_hail_integration = true
+        String hail_wheel = "gs://gvs-internal-scratch/hail-wheels/2022-10-18/0.2.102-964bee061eb0/hail-0.2.102-py3-none-any.whl"
     }
 
-    # Only assert identical outputs if we did not filter (filtering is not deterministic)
-    if (extract_do_not_filter_override) {
-        call AssertIdenticalOutputs {
-            input:
-                expected_output_prefix = expected_output_prefix,
-                actual_vcfs = GvsUnified.output_vcfs
-        }
+    String project_id = "gvs-internal"
 
-        call AssertCostIsTrackedAndExpected {
+    if (run_hail_integration) {
+        call QuickstartHailIntegration.GvsQuickstartHailIntegration {
             input:
-                go = GvsUnified.done,
-                dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-                project_id = project_id,
-                expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
+                branch_name = branch_name,
+                hail_wheel = hail_wheel,
         }
+    }
 
-        call AssertTableSizesAreExpected {
+    if (run_vcf_integration) {
+        call QuickstartVcfIntegration.GvsQuickstartVcfIntegration {
             input:
-                go = GvsUnified.done,
-                dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
-                project_id = project_id,
-                expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
+                branch_name = branch_name,
         }
     }
-
-    output {
-        Array[File] output_vcfs = GvsUnified.output_vcfs
-        Array[File] output_vcf_indexes = GvsUnified.output_vcf_indexes
-        Float total_vcfs_size_mb = GvsUnified.total_vcfs_size_mb
-        File manifest = GvsUnified.manifest
-        String dataset_name = BuildGATKJarAndCreateDataset.dataset_name
-        String filter_set_name = "quickit"
-        Boolean done = true
-    }
-}
-
-
-task AssertIdenticalOutputs {
-    input {
-        String expected_output_prefix
-        Array[File] actual_vcfs
-    }
-
-    command <<<
-        set -o errexit
-        set -o nounset
-        set -o pipefail
-
-        failures=()
-
-        # Where the current set of expected results lives in the cloud
-        expected_prefix="~{expected_output_prefix}"
-        # Remove a trailing slash if there is one
-        expected_prefix=${expected_prefix%/}
-
-        # Download all the expected data
-        mkdir expected
-        cd expected
-        # Make a FOFN for more efficient downloading
-        for file in ~{sep= ' ' actual_vcfs}; do
-            echo "$expected_prefix/$(basename $file)" >> expected_fofn.txt
-        done
-        # Download and unzip all the expected data
-        cat expected_fofn.txt | gsutil -m cp -I .
-        gzip -d *.gz
-        cd ..
-
-        # Also unzip actual result data
-        gzip -d ~{sep= ' ' actual_vcfs}
-
-        # Headers first, these can yield useful diagnostics when there are mismatches.
-        for file in ~{sep=' ' actual_vcfs}; do
-          unzipped=${file%.gz}
-          expected="expected/$(basename $unzipped)"
-          set +o errexit
-          cmp <(grep '^#' $unzipped) <(grep '^#' $expected)
-          rc=$?
-          set -o errexit
-          if [[ $rc -ne 0 ]]; then
-            # If there is a mismatch add it to a list of failures but keep on looking for mismatches.
-            failures+=( $unzipped )
-          fi
-        done
-
-        if [[ ${#failures[@]} -ne 0 ]]; then
-          echo "Error: headers for the following files do not match:"
-          for failure in ${failures[@]}; do
-            echo $(basename $failure)
-            expected="expected/$(basename $failure)"
-            diff $failure $expected
-          done
-          exit 1
-        fi
-
-        # If the headers all matched look for any mismatches in overall file content.
-        fail=0
-        for file in ~{sep=' ' actual_vcfs}; do
-          unzipped=${file%.gz}
-          expected="expected/$(basename $unzipped)"
-          set +o errexit
-          cmp $unzipped $expected
-          rc=$?
-          set -o errexit
-          if [[ $rc -ne 0 ]]; then
-            echo "Error: file contents of expected and actual do not match: $(basename $unzipped)"
-            fail=1
-          fi
-        done
-
-        if [[ $fail -ne 0 ]]; then
-          exit 1
-        fi
-
-        echo "All vcfs compared and matched!"
-    >>>
-
-    runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
-        disks: "local-disk 500 HDD"
-    }
-
-    output {
-        File fofn = "expected/expected_fofn.txt"
-        Boolean done = true
-    }
-}
-
-task AssertCostIsTrackedAndExpected {
-    meta {
-        # we want to check the database each time this runs
-        volatile: true
-    }
-
-    input {
-        Boolean go = true
-        String dataset_name
-        String project_id
-        File expected_output_csv
-    }
-
-    command <<<
-        set -o errexit
-        set -o nounset
-        set -o pipefail
-
-        echo "project_id = ~{project_id}" > ~/.bigqueryrc
-        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
-            "SELECT call, step, event_key, sum(event_bytes) \
-              FROM \`~{dataset_name}.cost_observability\` \
-              GROUP BY call, step, event_key \
-              ORDER BY call, step, event_key" > cost_observability_output.csv
-
-        # Put the exit code in a file because we are using a subshell (while) later and changes to the variable *in* the subshell are lost
-        echo "0" > ret_val.txt
-
-        paste cost_observability_output.csv ~{expected_output_csv} | while  IFS=$'\t' read observed expected; do
-        IFS=, read -ra OBS <<< "$observed"
-        IFS=, read -ra EXP <<< "$expected"
-        if [[ "${#OBS[@]}" -ne 4  || "${#EXP[@]}" -ne 4 ]]; then
-          echo "Unexpected number of rows found in the input files"
-          exit 1
-        fi
-
-        OBS_KEY=${OBS[0]}.${OBS[1]}.${OBS[2]}
-        EXP_KEY=${EXP[0]}.${EXP[1]}.${EXP[2]}
-        if [[ "$OBS_KEY" != "$EXP_KEY" ]]; then
-          echo "Mismatched keys in results files - were these sorted properly?"
-          exit 1
-        fi
-
-        if [[ "$OBS_KEY" == "call.step.event_key" ]]; then
-          # Skip the header
-          continue;
-        fi
-
-        OBS_BYTES=${OBS[3]}
-        EXP_BYTES=${EXP[3]}
-
-        TOLERANCE=0
-
-        # For these two costs, there is non-determinism in the pipeline - we allow a % difference
-        if [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.BigQuery Query Scanned" ]]; then
-          TOLERANCE=0.015   # 1.5% tolerance  (Note - have seen as high as: 0.0109429)
-        elif [[ $OBS_KEY == "ExtractTask.GvsCreateCallset.Storage API Scanned" ]]; then
-          TOLERANCE=0.01   # 1% tolerance  (Note - have seen as high as: 0.00608656)
-        elif [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.Storage API Scanned" ]]; then
-          TOLERANCE=0.05  # 5% tolerance (Note - have seen as high as: 0.0281223)
-        fi
-
-        if [[ $OBS_BYTES -ne $EXP_BYTES ]]; then
-          echo "The bytes observed ($OBS_BYTES) for '$OBS_KEY' differ from those expected ($EXP_BYTES)"
-
-          if [[ $OBS_BYTES -ge $EXP_BYTES ]]; then
-            DIFF_FOUND=$(echo $OBS_BYTES $EXP_BYTES | awk '{print ($1-$2)/$1}')
-          else
-            DIFF_FOUND=$(echo $EXP_BYTES $OBS_BYTES | awk '{print ($1-$2)/$1}')
-          fi
-
-          if ! awk "BEGIN{ exit ($DIFF_FOUND > $TOLERANCE) }"
-          then
-            echo "FAIL!!! The relative difference between these is $DIFF_FOUND, which is greater than the allowed tolerance ($TOLERANCE)"
-            echo "1" > ret_val.txt
-          else
-            echo "However, the relative difference between these is $DIFF_FOUND, which is below the allowed tolerance ($TOLERANCE)"
-          fi
-        fi
-        done
-
-        RET_VAL=`cat ret_val.txt`
-        exit $RET_VAL
-
-    >>>
-
-    runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
-        disks: "local-disk 10 HDD"
-    }
-
-    output {
-        File cost_observability_output_csv = "cost_observability_output.csv"
-    }
-}
-
-task AssertTableSizesAreExpected {
-    meta {
-        # we want to check the database each time this runs
-        volatile: true
-    }
-
-    input {
-        Boolean go = true
-        String dataset_name
-        String project_id
-        File expected_output_csv
-    }
-
-    command <<<
-        set -o errexit
-        set -o nounset
-        set -o pipefail
-
-        echo "project_id = ~{project_id}" > ~/.bigqueryrc
-        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
-            "SELECT 'vet_total' AS total_name, sum(total_billable_bytes) AS total_bytes FROM \
-            \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` WHERE table_name LIKE 'vet_%' \
-            UNION ALL \
-            SELECT 'ref_ranges_total' AS total_name, sum(total_billable_bytes) AS total_bytes \
-            FROM \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` \
-            WHERE table_name LIKE 'ref_ranges_%' ORDER BY total_name" > table_size_output.csv
-
-        set +o errexit
-        diff -w table_size_output.csv ~{expected_output_csv} > differences.txt
-        set -o errexit
-
-        if [[ -s differences.txt ]]; then
-            echo "Differences found:"
-            cat differences.txt
-            exit 1
-        fi
-    >>>
-
-    runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
-        disks: "local-disk 10 HDD"
-    }
-
-    output {
-        File table_size_output_csv = "table_size_output.csv"
-        File differences = "differences.txt"
-    }
 }
diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
new file mode 100644
index 00000000000..dc4e7efb7c8
--- /dev/null
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -0,0 +1,351 @@
+version 1.0
+
+import "GvsUnified.wdl" as Unified
+import "GvsUtils.wdl" as Utils
+
+workflow GvsQuickstartVcfIntegration {
+
+    input {
+        String branch_name
+        String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-10-20/"
+
+        Array[String] external_sample_names = [
+                                              "ERS4367795",
+                                              "ERS4367796",
+                                              "ERS4367797",
+                                              "ERS4367798",
+                                              "ERS4367799",
+                                              "ERS4367800",
+                                              "ERS4367801",
+                                              "ERS4367803",
+                                              "ERS4367804",
+                                              "ERS4367805"
+                                              ]
+
+        Array[File] input_vcfs = [
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz",
+                                 "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz"
+                                 ]
+
+        Array[File] input_vcf_indexes = [
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00408.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00418.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00420.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00423.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00427.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00429.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00444.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00447.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi",
+                                        "gs://gvs-internal-quickstart/reblocked-v2-vcfs/HG00450.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz.tbi"
+                                        ]
+
+        Int? extract_scatter_count
+        String drop_state = "FORTY"
+        Boolean extract_do_not_filter_override = true
+    }
+    String project_id = "gvs-internal"
+
+    call Utils.BuildGATKJarAndCreateDataset {
+        input:
+            branch_name = branch_name,
+            dataset_prefix = "quickit"
+    }
+
+    call Unified.GvsUnified {
+        input:
+            call_set_identifier = branch_name,
+            dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+            project_id = project_id,
+            external_sample_names = external_sample_names,
+            gatk_override = BuildGATKJarAndCreateDataset.jar,
+            input_vcfs = input_vcfs,
+            input_vcf_indexes = input_vcf_indexes,
+            filter_set_name = "quickit",
+            extract_table_prefix = "quickit",
+            extract_scatter_count = extract_scatter_count,
+            # Force filtering off as it is not deterministic and the initial version of this integration test does not
+            # allow for inexact matching of actual and expected results.
+            extract_do_not_filter_override = extract_do_not_filter_override,
+            drop_state = drop_state
+    }
+
+    # Only assert identical outputs if we did not filter (filtering is not deterministic)
+    if (extract_do_not_filter_override) {
+        call AssertIdenticalOutputs {
+            input:
+                expected_output_prefix = expected_output_prefix,
+                actual_vcfs = GvsUnified.output_vcfs
+        }
+
+        call AssertCostIsTrackedAndExpected {
+            input:
+                go = GvsUnified.done,
+                dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+                project_id = project_id,
+                expected_output_csv = expected_output_prefix + "cost_observability_expected.csv"
+        }
+
+        call AssertTableSizesAreExpected {
+            input:
+                go = GvsUnified.done,
+                dataset_name = BuildGATKJarAndCreateDataset.dataset_name,
+                project_id = project_id,
+                expected_output_csv = expected_output_prefix + "table_sizes_expected.csv"
+        }
+    }
+
+    output {
+        Array[File] output_vcfs = GvsUnified.output_vcfs
+        Array[File] output_vcf_indexes = GvsUnified.output_vcf_indexes
+        Float total_vcfs_size_mb = GvsUnified.total_vcfs_size_mb
+        File manifest = GvsUnified.manifest
+        String dataset_name = BuildGATKJarAndCreateDataset.dataset_name
+        String filter_set_name = "quickit"
+        Boolean done = true
+    }
+}
+
+
+task AssertIdenticalOutputs {
+    input {
+        String expected_output_prefix
+        Array[File] actual_vcfs
+    }
+
+    command <<<
+        set -o errexit
+        set -o nounset
+        set -o pipefail
+
+        failures=()
+
+        # Where the current set of expected results lives in the cloud
+        expected_prefix="~{expected_output_prefix}"
+        # Remove a trailing slash if there is one
+        expected_prefix=${expected_prefix%/}
+
+        # Download all the expected data
+        mkdir expected
+        cd expected
+        # Make a FOFN for more efficient downloading
+        for file in ~{sep= ' ' actual_vcfs}; do
+            echo "$expected_prefix/$(basename $file)" >> expected_fofn.txt
+        done
+        # Download and unzip all the expected data
+        cat expected_fofn.txt | gsutil -m cp -I .
+        gzip -d *.gz
+        cd ..
+
+        # Also unzip actual result data
+        gzip -d ~{sep= ' ' actual_vcfs}
+
+        # Headers first, these can yield useful diagnostics when there are mismatches.
+        for file in ~{sep=' ' actual_vcfs}; do
+          unzipped=${file%.gz}
+          expected="expected/$(basename $unzipped)"
+          set +o errexit
+          cmp <(grep '^#' $unzipped) <(grep '^#' $expected)
+          rc=$?
+          set -o errexit
+          if [[ $rc -ne 0 ]]; then
+            # If there is a mismatch add it to a list of failures but keep on looking for mismatches.
+            failures+=( $unzipped )
+          fi
+        done
+
+        if [[ ${#failures[@]} -ne 0 ]]; then
+          echo "Error: headers for the following files do not match:"
+          for failure in ${failures[@]}; do
+            echo $(basename $failure)
+            expected="expected/$(basename $failure)"
+            diff $failure $expected
+          done
+          exit 1
+        fi
+
+        # If the headers all matched look for any mismatches in overall file content.
+        fail=0
+        for file in ~{sep=' ' actual_vcfs}; do
+          unzipped=${file%.gz}
+          expected="expected/$(basename $unzipped)"
+          set +o errexit
+          cmp $unzipped $expected
+          rc=$?
+          set -o errexit
+          if [[ $rc -ne 0 ]]; then
+            echo "Error: file contents of expected and actual do not match: $(basename $unzipped)"
+            fail=1
+          fi
+        done
+
+        if [[ $fail -ne 0 ]]; then
+          exit 1
+        fi
+
+        echo "All vcfs compared and matched!"
+    >>>
+
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
+        disks: "local-disk 500 HDD"
+    }
+
+    output {
+        File fofn = "expected/expected_fofn.txt"
+        Boolean done = true
+    }
+}
+
+task AssertCostIsTrackedAndExpected {
+    meta {
+        # we want to check the database each time this runs
+        volatile: true
+    }
+
+    input {
+        Boolean go = true
+        String dataset_name
+        String project_id
+        File expected_output_csv
+    }
+
+    command <<<
+        set -o errexit
+        set -o nounset
+        set -o pipefail
+
+        echo "project_id = ~{project_id}" > ~/.bigqueryrc
+        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
+            "SELECT call, step, event_key, sum(event_bytes) \
+              FROM \`~{dataset_name}.cost_observability\` \
+              GROUP BY call, step, event_key \
+              ORDER BY call, step, event_key" > cost_observability_output.csv
+
+        # Put the exit code in a file because we are using a subshell (while) later and changes to the variable *in* the subshell are lost
+        echo "0" > ret_val.txt
+
+        paste cost_observability_output.csv ~{expected_output_csv} | while  IFS=$'\t' read observed expected; do
+        IFS=, read -ra OBS <<< "$observed"
+        IFS=, read -ra EXP <<< "$expected"
+        if [[ "${#OBS[@]}" -ne 4  || "${#EXP[@]}" -ne 4 ]]; then
+          echo "Unexpected number of rows found in the input files"
+          exit 1
+        fi
+
+        OBS_KEY=${OBS[0]}.${OBS[1]}.${OBS[2]}
+        EXP_KEY=${EXP[0]}.${EXP[1]}.${EXP[2]}
+        if [[ "$OBS_KEY" != "$EXP_KEY" ]]; then
+          echo "Mismatched keys in results files - were these sorted properly?"
+          exit 1
+        fi
+
+        if [[ "$OBS_KEY" == "call.step.event_key" ]]; then
+          # Skip the header
+          continue;
+        fi
+
+        OBS_BYTES=${OBS[3]}
+        EXP_BYTES=${EXP[3]}
+
+        TOLERANCE=0
+
+        # For these two costs, there is non-determinism in the pipeline - we allow a % difference
+        if [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.BigQuery Query Scanned" ]]; then
+          TOLERANCE=0.015   # 1.5% tolerance  (Note - have seen as high as: 0.0109429)
+        elif [[ $OBS_KEY == "ExtractTask.GvsCreateCallset.Storage API Scanned" ]]; then
+          TOLERANCE=0.01   # 1% tolerance  (Note - have seen as high as: 0.00608656)
+        elif [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.Storage API Scanned" ]]; then
+          TOLERANCE=0.05  # 5% tolerance (Note - have seen as high as: 0.0281223)
+        fi
+
+        if [[ $OBS_BYTES -ne $EXP_BYTES ]]; then
+          echo "The bytes observed ($OBS_BYTES) for '$OBS_KEY' differ from those expected ($EXP_BYTES)"
+
+          if [[ $OBS_BYTES -ge $EXP_BYTES ]]; then
+            DIFF_FOUND=$(echo $OBS_BYTES $EXP_BYTES | awk '{print ($1-$2)/$1}')
+          else
+            DIFF_FOUND=$(echo $EXP_BYTES $OBS_BYTES | awk '{print ($1-$2)/$1}')
+          fi
+
+          if ! awk "BEGIN{ exit ($DIFF_FOUND > $TOLERANCE) }"
+          then
+            echo "FAIL!!! The relative difference between these is $DIFF_FOUND, which is greater than the allowed tolerance ($TOLERANCE)"
+            echo "1" > ret_val.txt
+          else
+            echo "However, the relative difference between these is $DIFF_FOUND, which is below the allowed tolerance ($TOLERANCE)"
+          fi
+        fi
+        done
+
+        RET_VAL=`cat ret_val.txt`
+        exit $RET_VAL
+
+    >>>
+
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
+        disks: "local-disk 10 HDD"
+    }
+
+    output {
+        File cost_observability_output_csv = "cost_observability_output.csv"
+    }
+}
+
+task AssertTableSizesAreExpected {
+    meta {
+        # we want to check the database each time this runs
+        volatile: true
+    }
+
+    input {
+        Boolean go = true
+        String dataset_name
+        String project_id
+        File expected_output_csv
+    }
+
+    command <<<
+        set -o errexit
+        set -o nounset
+        set -o pipefail
+
+        echo "project_id = ~{project_id}" > ~/.bigqueryrc
+        bq query --project_id=~{project_id} --format=csv --use_legacy_sql=false \
+            "SELECT 'vet_total' AS total_name, sum(total_billable_bytes) AS total_bytes FROM \
+            \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` WHERE table_name LIKE 'vet_%' \
+            UNION ALL \
+            SELECT 'ref_ranges_total' AS total_name, sum(total_billable_bytes) AS total_bytes \
+            FROM \`~{dataset_name}.INFORMATION_SCHEMA.PARTITIONS\` \
+            WHERE table_name LIKE 'ref_ranges_%' ORDER BY total_name" > table_size_output.csv
+
+        set +o errexit
+        diff -w table_size_output.csv ~{expected_output_csv} > differences.txt
+        set -o errexit
+
+        if [[ -s differences.txt ]]; then
+            echo "Differences found:"
+            cat differences.txt
+            exit 1
+        fi
+    >>>
+
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:402.0.0-alpine"
+        disks: "local-disk 10 HDD"
+    }
+
+    output {
+        File table_size_output_csv = "table_size_output.csv"
+        File differences = "differences.txt"
+    }
+}
diff --git a/scripts/variantstore/wdl/extract/test_workflow_compute_costs.py b/scripts/variantstore/wdl/extract/test_workflow_compute_costs.py
index f1df87ca14c..23b6c40726b 100644
--- a/scripts/variantstore/wdl/extract/test_workflow_compute_costs.py
+++ b/scripts/variantstore/wdl/extract/test_workflow_compute_costs.py
@@ -77,7 +77,7 @@ def test_all_submissions(self):
                               )
 
         self.assertEqual(self.__count_gvs_workflows(costs), 2, msg="Expecting exactly two workflow names in costs dictionary")
-        integration = costs['GvsQuickstartIntegration']
+        integration = costs['GvsQuickstartVcfIntegration']
 
         expected = [{'cost': 0.885638,
                      'link': 'https://app.terra.bio/#workspaces/test_workspace_namespace/test_workspace/job_history/73ac71db-0488-46be-a8e8-7f00e795edec',
@@ -115,7 +115,7 @@ def test_apply_exclusion(self):
 
         self.assertEqual(self.__count_gvs_workflows(costs), 2, msg="Expecting exactly two kinds of workflows in costs dictionary")
 
-        integration = costs['GvsQuickstartIntegration']
+        integration = costs['GvsQuickstartVcfIntegration']
         expected = [{'cost': 0.885638,
                      'link': 'https://app.terra.bio/#workspaces/test_workspace_namespace/test_workspace/job_history/73ac71db-0488-46be-a8e8-7f00e795edec',
                      'submission_id': '73ac71db-0488-46be-a8e8-7f00e795edec',
diff --git a/scripts/variantstore/wdl/extract/workflow_compute_costs_test_helper.py b/scripts/variantstore/wdl/extract/workflow_compute_costs_test_helper.py
index 8dee7d1ec95..dc2527f62cc 100644
--- a/scripts/variantstore/wdl/extract/workflow_compute_costs_test_helper.py
+++ b/scripts/variantstore/wdl/extract/workflow_compute_costs_test_helper.py
@@ -1,14 +1,14 @@
 FAILED_INTEGRATION_SUBMISSION_ID = '136781a2-64b8-4ede-8652-973136030aaf'
 
 FAILED_INTEGRATION_SUBMISSION = {'cost': 0.104732, 'deleteIntermediateOutputFiles': False, 'memoryRetryMultiplier': 1,
-                                 'methodConfigurationName': 'GvsQuickstartIntegration',
+                                 'methodConfigurationName': 'GvsQuickstartVcfIntegration',
                                  'methodConfigurationNamespace': 'method-config-namespace', 'status': 'Done',
                                  'submissionDate': '2022-06-09T20:28:57.797Z',
                                  'submissionId': '136781a2-64b8-4ede-8652-973136030aaf',
                                  'submitter': 'gumby@broadinstitute.org', 'useCallCache': False,
                                  'useReferenceDisks': False, 'userComment': '', 'workflows': [{'cost': 0.104732,
                                                                                                'inputResolutions': [{
-                                                                                                   'inputName': 'GvsQuickstartIntegration.branch_name',
+                                                                                                   'inputName': 'GvsQuickstartVcfIntegration.branch_name',
                                                                                                    'value': 'vs_447_fixup_non_fq_invocations'}],
                                                                                                'messages': [],
                                                                                                'status': 'Failed',
@@ -16,7 +16,7 @@
                                                                                                'workflowId': '902df806-5852-43d0-9816-ff46bf7e1716'}]}
 
 FAILED_INTEGRATION_WORKFLOW = {
-    "workflowName": "GvsQuickstartIntegration",
+    "workflowName": "GvsQuickstartVcfIntegration",
     "id": "902df806-5852-43d0-9816-ff46bf7e1716",
     "actualWorkflowLanguage": "WDL",
     "actualWorkflowLanguageVersion": "1.0"
@@ -26,14 +26,14 @@
 
 SUCCEEDED_INTEGRATION_SUBMISSION = {'cost': 0.885638, 'deleteIntermediateOutputFiles': False,
                                     'memoryRetryMultiplier': 1,
-                                    'methodConfigurationName': 'GvsQuickstartIntegration',
+                                    'methodConfigurationName': 'GvsQuickstartVcfIntegration',
                                     'methodConfigurationNamespace': 'method-config-namespace', 'status': 'Done',
                                     'submissionDate': '2022-06-10T10:22:34.320Z',
                                     'submissionId': '73ac71db-0488-46be-a8e8-7f00e795edec',
                                     'submitter': 'gumby@broadinstitute.org', 'useCallCache': False,
                                     'useReferenceDisks': False,
                                     'userComment': '', 'workflows': [{'cost': 0.885638, 'inputResolutions': [
-        {'inputName': 'GvsQuickstartIntegration.branch_name', 'value': 'vs_447_fixup_non_fq_invocations'}],
+        {'inputName': 'GvsQuickstartVcfIntegration.branch_name', 'value': 'vs_447_fixup_non_fq_invocations'}],
                                                                       'messages': [], 'status': 'Succeeded',
                                                                       'statusLastChangedDate': '2022-06-10T14:27:54.958Z',
                                                                       'workflowId': 'a7e9cf65-f3e6-4ede-b64e-38018ca560f3'}]}
@@ -76,7 +76,7 @@
                                                                                                  'workflowId': 'e3120691-cf45-471d-85d8-a10a8ef51a07'}]}
 
 SUCCEEDED_INTEGRATION_WORKFLOW = {
-    "workflowName": "GvsQuickstartIntegration",
+    "workflowName": "GvsQuickstartVcfIntegration",
     "id": "a7e9cf65-f3e6-4ede-b64e-38018ca560f3",
     "actualWorkflowLanguage": "WDL",
     "actualWorkflowLanguageVersion": "1.0"

From 08ebbccd6de55538b64527e192138ae22933e254 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 15:50:23 -0400
Subject: [PATCH 35/49] separate test run prefixes

---
 .../variantstore/wdl/GvsQuickstartHailIntegration.wdl    | 1 +
 scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl | 9 +++++----
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index c80d5eb135f..e878891e730 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -17,6 +17,7 @@ workflow GvsQuickstartHailIntegration {
             branch_name = branch_name,
             drop_state = "NONE",
             extract_do_not_filter_override = false,
+            test_run_prefix = "quickit_hail",
     }
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
index dc4e7efb7c8..29e4aa04a55 100644
--- a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -7,6 +7,7 @@ workflow GvsQuickstartVcfIntegration {
 
     input {
         String branch_name
+        String test_run_prefix = "quickit_vcf"
         String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-10-20/"
 
         Array[String] external_sample_names = [
@@ -57,7 +58,7 @@ workflow GvsQuickstartVcfIntegration {
     call Utils.BuildGATKJarAndCreateDataset {
         input:
             branch_name = branch_name,
-            dataset_prefix = "quickit"
+            dataset_prefix = test_run_prefix,
     }
 
     call Unified.GvsUnified {
@@ -69,8 +70,8 @@ workflow GvsQuickstartVcfIntegration {
             gatk_override = BuildGATKJarAndCreateDataset.jar,
             input_vcfs = input_vcfs,
             input_vcf_indexes = input_vcf_indexes,
-            filter_set_name = "quickit",
-            extract_table_prefix = "quickit",
+            filter_set_name = test_run_prefix,
+            extract_table_prefix = test_run_prefix,
             extract_scatter_count = extract_scatter_count,
             # Force filtering off as it is not deterministic and the initial version of this integration test does not
             # allow for inexact matching of actual and expected results.
@@ -109,7 +110,7 @@ workflow GvsQuickstartVcfIntegration {
         Float total_vcfs_size_mb = GvsUnified.total_vcfs_size_mb
         File manifest = GvsUnified.manifest
         String dataset_name = BuildGATKJarAndCreateDataset.dataset_name
-        String filter_set_name = "quickit"
+        String filter_set_name = test_run_prefix
         Boolean done = true
     }
 }

From 86c6e9b439631d3203b92176d6ef0a1f5632fb1b Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 20:07:50 -0400
Subject: [PATCH 36/49] cleanup

---
 .../wdl/GvsQuickstartVcfIntegration.wdl             | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
index 29e4aa04a55..413c7d7ee2c 100644
--- a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -123,9 +123,9 @@ task AssertIdenticalOutputs {
     }
 
     command <<<
-        set -o errexit
-        set -o nounset
-        set -o pipefail
+        # Prepend date, time and pwd to xtrace log entries.
+        PS4='\D{+%F %T} \w $ '
+        set -o errexit -o nounset -o pipefail -o xtrace
 
         failures=()
 
@@ -137,12 +137,7 @@ task AssertIdenticalOutputs {
         # Download all the expected data
         mkdir expected
         cd expected
-        # Make a FOFN for more efficient downloading
-        for file in ~{sep= ' ' actual_vcfs}; do
-            echo "$expected_prefix/$(basename $file)" >> expected_fofn.txt
-        done
-        # Download and unzip all the expected data
-        cat expected_fofn.txt | gsutil -m cp -I .
+        gcloud storage cp -r "${expected_prefix}"'/*.vcf.gz' .
         gzip -d *.gz
         cd ..
 

From b0b11608357f8a4191555c20bc74d497048fab22 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 20:08:34 -0400
Subject: [PATCH 37/49] Revert "separate test run prefixes"

This reverts commit 69467cbfbd21cab77c4366a49a4b208f5dae8f5c.
---
 .../variantstore/wdl/GvsQuickstartHailIntegration.wdl    | 1 -
 scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl | 9 ++++-----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index e878891e730..c80d5eb135f 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -17,7 +17,6 @@ workflow GvsQuickstartHailIntegration {
             branch_name = branch_name,
             drop_state = "NONE",
             extract_do_not_filter_override = false,
-            test_run_prefix = "quickit_hail",
     }
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
index 413c7d7ee2c..61caf5b5ec7 100644
--- a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -7,7 +7,6 @@ workflow GvsQuickstartVcfIntegration {
 
     input {
         String branch_name
-        String test_run_prefix = "quickit_vcf"
         String expected_output_prefix = "gs://gvs-internal-quickstart/integration/2022-10-20/"
 
         Array[String] external_sample_names = [
@@ -58,7 +57,7 @@ workflow GvsQuickstartVcfIntegration {
     call Utils.BuildGATKJarAndCreateDataset {
         input:
             branch_name = branch_name,
-            dataset_prefix = test_run_prefix,
+            dataset_prefix = "quickit"
     }
 
     call Unified.GvsUnified {
@@ -70,8 +69,8 @@ workflow GvsQuickstartVcfIntegration {
             gatk_override = BuildGATKJarAndCreateDataset.jar,
             input_vcfs = input_vcfs,
             input_vcf_indexes = input_vcf_indexes,
-            filter_set_name = test_run_prefix,
-            extract_table_prefix = test_run_prefix,
+            filter_set_name = "quickit",
+            extract_table_prefix = "quickit",
             extract_scatter_count = extract_scatter_count,
             # Force filtering off as it is not deterministic and the initial version of this integration test does not
             # allow for inexact matching of actual and expected results.
@@ -110,7 +109,7 @@ workflow GvsQuickstartVcfIntegration {
         Float total_vcfs_size_mb = GvsUnified.total_vcfs_size_mb
         File manifest = GvsUnified.manifest
         String dataset_name = BuildGATKJarAndCreateDataset.dataset_name
-        String filter_set_name = test_run_prefix
+        String filter_set_name = "quickit"
         Boolean done = true
     }
 }

From a228651987ffe4733c2c397759da56c75193eddb Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 3 Nov 2022 20:13:18 -0400
Subject: [PATCH 38/49] rework

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 1 +
 scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl  | 4 +++-
 scripts/variantstore/wdl/GvsUtils.wdl                     | 3 ++-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index c80d5eb135f..27e7f6bde2b 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -17,6 +17,7 @@ workflow GvsQuickstartHailIntegration {
             branch_name = branch_name,
             drop_state = "NONE",
             extract_do_not_filter_override = false,
+            dataset_suffix = "hail",
     }
 
     call ExtractAvroFilesForHail.GvsExtractAvroFilesForHail {
diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
index 61caf5b5ec7..4779e6dde5d 100644
--- a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -51,13 +51,15 @@ workflow GvsQuickstartVcfIntegration {
         Int? extract_scatter_count
         String drop_state = "FORTY"
         Boolean extract_do_not_filter_override = true
+        String dataset_suffix = "vcf"
     }
     String project_id = "gvs-internal"
 
     call Utils.BuildGATKJarAndCreateDataset {
         input:
             branch_name = branch_name,
-            dataset_prefix = "quickit"
+            dataset_prefix = "quickit",
+            dataset_suffix = dataset_suffix,
     }
 
     call Unified.GvsUnified {
diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl
index e1b9317cbe4..07aaf7c89df 100644
--- a/scripts/variantstore/wdl/GvsUtils.wdl
+++ b/scripts/variantstore/wdl/GvsUtils.wdl
@@ -214,6 +214,7 @@ task BuildGATKJarAndCreateDataset {
   input {
     String branch_name
     String dataset_prefix
+    String dataset_suffix
   }
   meta {
     # Branch may be updated so do not call cache!
@@ -263,7 +264,7 @@ task BuildGATKJarAndCreateDataset {
     # Build a dataset name based on the branch name and the git hash of the most recent commit on this branch.
     # Dataset names must be alphanumeric and underscores only. Convert any dashes to underscores, then delete
     # any remaining characters that are not alphanumeric or underscores.
-    dataset="$(echo ~{dataset_prefix}_${branch}_${hash} | tr '-' '_' | tr -c -d '[:alnum:]_')"
+    dataset="$(echo ~{dataset_prefix}_${branch}_${hash}_~{dataset_suffix} | tr '-' '_' | tr -c -d '[:alnum:]_')"
 
     bq mk --project_id="gvs-internal" "$dataset"
 

From 80eb98364cc9c5d600d9d011dc180ce59b1f63c3 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Fri, 4 Nov 2022 04:17:45 -0400
Subject: [PATCH 39/49] fixes / improvements

---
 .../wdl/GvsQuickstartVcfIntegration.wdl       | 21 +++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
index 4779e6dde5d..1185cd55520 100644
--- a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -122,7 +122,11 @@ task AssertIdenticalOutputs {
         String expected_output_prefix
         Array[File] actual_vcfs
     }
-
+    parameter_meta {
+        actual_vcfs: {
+            localization_optional: true
+        }
+    }
     command <<<
         # Prepend date, time and pwd to xtrace log entries.
         PS4='\D{+%F %T} \w $ '
@@ -142,8 +146,18 @@ task AssertIdenticalOutputs {
         gzip -d *.gz
         cd ..
 
-        # Also unzip actual result data
-        gzip -d ~{sep= ' ' actual_vcfs}
+        touch actual_manifest.txt
+        # Making the manifest is pretty uninteresting and very noisy so turn off xtrace temporarily.
+        set +o xtrace
+        for file in ~{actual_vcfs}
+        do
+            echo $file >> actual_manifest.txt
+        done
+
+        set -o xtrace
+        cat actual_manifest.txt | gcloud storage cp -I .
+        # Unzip actual result data.
+        ls -1 | grep -E '\.vcf\.gz$' | xargs gzip -d
 
         # Headers first, these can yield useful diagnostics when there are mismatches.
         for file in ~{sep=' ' actual_vcfs}; do
@@ -197,7 +211,6 @@ task AssertIdenticalOutputs {
     }
 
     output {
-        File fofn = "expected/expected_fofn.txt"
         Boolean done = true
     }
 }

From 901a3edc920213ad8c07492a65a5040a90e31ba1 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Fri, 4 Nov 2022 11:20:17 -0400
Subject: [PATCH 40/49] gah

---
 scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
index 1185cd55520..bac1de14e68 100644
--- a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -149,7 +149,7 @@ task AssertIdenticalOutputs {
         touch actual_manifest.txt
         # Making the manifest is pretty uninteresting and very noisy so turn off xtrace temporarily.
         set +o xtrace
-        for file in ~{actual_vcfs}
+        for file in ~{sep=' ' actual_vcfs}
         do
             echo $file >> actual_manifest.txt
         done

From c49641afcabd9b49de1d2a879a3d043eae3f4543 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Mon, 7 Nov 2022 14:43:54 -0500
Subject: [PATCH 41/49] oops

---
 .../wdl/GvsQuickstartVcfIntegration.wdl       | 40 +++++++++++--------
 1 file changed, 23 insertions(+), 17 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
index bac1de14e68..d37e57835d6 100644
--- a/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
@@ -146,54 +146,60 @@ task AssertIdenticalOutputs {
         gzip -d *.gz
         cd ..
 
+        mkdir actual
+        cd actual
         touch actual_manifest.txt
         # Making the manifest is pretty uninteresting and very noisy so turn off xtrace temporarily.
         set +o xtrace
-        for file in ~{sep=' ' actual_vcfs}
+        for actual in ~{sep=' ' actual_vcfs}
         do
-            echo $file >> actual_manifest.txt
+            echo $actual >> actual_manifest.txt
         done
-
         set -o xtrace
+
         cat actual_manifest.txt | gcloud storage cp -I .
         # Unzip actual result data.
         ls -1 | grep -E '\.vcf\.gz$' | xargs gzip -d
+        cd ..
 
         # Headers first, these can yield useful diagnostics when there are mismatches.
-        for file in ~{sep=' ' actual_vcfs}; do
-          unzipped=${file%.gz}
-          expected="expected/$(basename $unzipped)"
+        for vcf in $(ls -1 actual | grep -E '\.vcf$')
+        do
+          actual="actual/$vcf"
+          expected="expected/$vcf"
           set +o errexit
-          cmp <(grep '^#' $unzipped) <(grep '^#' $expected)
+          cmp <(grep '^#' $actual) <(grep '^#' $expected)
           rc=$?
           set -o errexit
           if [[ $rc -ne 0 ]]; then
             # If there is a mismatch add it to a list of failures but keep on looking for mismatches.
-            failures+=( $unzipped )
+            failures+=( $vcf )
           fi
         done
 
         if [[ ${#failures[@]} -ne 0 ]]; then
           echo "Error: headers for the following files do not match:"
           for failure in ${failures[@]}; do
-            echo $(basename $failure)
-            expected="expected/$(basename $failure)"
-            diff $failure $expected
+            echo $failure
+            expected="expected/$failure"
+            actual="actual/$failure"
+            diff $actual $expected
           done
           exit 1
         fi
 
         # If the headers all matched look for any mismatches in overall file content.
         fail=0
-        for file in ~{sep=' ' actual_vcfs}; do
-          unzipped=${file%.gz}
-          expected="expected/$(basename $unzipped)"
+        for vcf in $(ls -1 | grep -E '\.vcf$')
+        do
+          expected="expected/$vcf"
+          actual="actual/$vcf"
           set +o errexit
-          cmp $unzipped $expected
+          cmp $actual $expected
           rc=$?
           set -o errexit
           if [[ $rc -ne 0 ]]; then
-            echo "Error: file contents of expected and actual do not match: $(basename $unzipped)"
+            echo "Error: file contents of expected and actual do not match: $vcf"
             fail=1
           fi
         done
@@ -270,7 +276,7 @@ task AssertCostIsTrackedAndExpected {
 
         # For these two costs, there is non-determinism in the pipeline - we allow a % difference
         if [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.BigQuery Query Scanned" ]]; then
-          TOLERANCE=0.015   # 1.5% tolerance  (Note - have seen as high as: 0.0109429)
+          TOLERANCE=0.02   # 2% tolerance  (Note - have seen as high as: 0.0157154)
         elif [[ $OBS_KEY == "ExtractTask.GvsCreateCallset.Storage API Scanned" ]]; then
           TOLERANCE=0.01   # 1% tolerance  (Note - have seen as high as: 0.00608656)
         elif [[ $OBS_KEY == "ExtractFilterTask.GvsCreateFilterSet.Storage API Scanned" ]]; then

From 98dcede015fd426f07f8df115c7c325bfb0aea27 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 8 Nov 2022 16:54:07 -0500
Subject: [PATCH 42/49] checkpoint

---
 .../wdl/extract/hail_gvs_import.py            | 155 +++++++-----------
 .../wdl/extract/test_hail_gvs_import.py       |   6 +-
 2 files changed, 64 insertions(+), 97 deletions(-)

diff --git a/scripts/variantstore/wdl/extract/hail_gvs_import.py b/scripts/variantstore/wdl/extract/hail_gvs_import.py
index 11fb138ac03..2d9d5f592d7 100644
--- a/scripts/variantstore/wdl/extract/hail_gvs_import.py
+++ b/scripts/variantstore/wdl/extract/hail_gvs_import.py
@@ -10,33 +10,45 @@
 gsutil -m cp 'gs://gvs-internal-scratch/hail-wheels/<date>-<short git hash>/hail-<Hail version>-py3-none-any.whl' .
 pip install --force-reinstall hail-<Hail version>-py3-none-any.whl
 ```
+"""
 
-* Additional non-cluster configuration:
 
-If running with a Spark cluster, setup should be complete. If running with a non-cluster environment,
-the following lines are required in the terminal:
+from google.cloud import storage
 
-```
-export PYSPARK_SUBMIT_ARGS='--driver-memory 16g --executor-memory 16g pyspark-shell'
-gcloud auth application-default login
-curl -sSL https://broad.io/install-gcs-connector | python3
-```
+import argparse
+import os
+import re
 
-* Running the GVS to Hail VDS conversion script:
+gcs_re = re.compile("^gs://(?P<bucket_name>[^/]+)/(?P<object_prefix>.*)$")
 
-`python hail_gvs_import.py`
 
-"""
+def init_hail(references_path, temp_path):
+    import hail as hl
+    hl.init(tmp_dir=f'{temp_path}/hail_tmp_general')
 
+    rg38 = hl.get_reference('GRCh38')
+    rg38.add_sequence(f'{references_path}/Homo_sapiens_assembly38.fasta.gz',
+                      f'{references_path}/Homo_sapiens_assembly38.fasta.fai')
+    return rg38
 
-from google.cloud import storage
 
-import argparse
-import os
-import re
+def import_gvs(argsfn, rg38, vds_path, temp_path):
+    import hail as hl
+
+    hl.import_gvs(
+        vets=argsfn('vets'),
+        refs=argsfn('refs'),
+        sample_mapping=argsfn('sample_mapping'),
+        site_filtering_data=argsfn('site_filtering_data'),
+        vqsr_filtering_data=argsfn('vqsr_filtering_data'),
+        vqsr_tranche_data=argsfn('vqsr_tranche_data'),
+        reference_genome=rg38,
+        final_path=vds_path,
+        tmp_dir=f'{temp_path}/hail_tmp_import_gvs',
+    )
 
 
-def generate_gcs_avro_args(bucket, blob_prefix, key):
+def gcs_generate_avro_args(bucket, blob_prefix, key):
     """
     Generate a list of the Avro arguments for the `hl.import_gvs` invocation for the specified key. The datatype should
     match the parameters of the `hl.import_gvs` function:
@@ -84,33 +96,19 @@ def regular_handler(blob_name):
     return ret
 
 
-def import_gvs_gcs(bucket, object_prefix, vds_output_path, tmp_dir):
-    import hail as hl
-
-    unslashed_tmp_dir = tmp_dir if not tmp_dir.endswith('/') else tmp_dir[:-1]
-    hl.init(tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_general')
+def gcs_import_gvs(avro_path, vds_path, temp_path):
+    rg38 = init_hail('gs://hail-common/references', temp_path)
 
-    rg38 = hl.get_reference('GRCh38')
-    rg38.add_sequence('gs://hail-common/references/Homo_sapiens_assembly38.fasta.gz',
-                      'gs://hail-common/references/Homo_sapiens_assembly38.fasta.fai')
+    avro_bucket_name, avro_object_prefix = gcs_re.match(avro_path).groups()
+    avro_bucket = storage.Client().get_bucket(avro_bucket_name)
 
     def args(key):
-        return generate_gcs_avro_args(bucket, object_prefix, key)
+        return gcs_generate_avro_args(avro_bucket, avro_object_prefix, key)
 
-    hl.import_gvs(
-        vets=args('vets'),
-        refs=args('refs'),
-        sample_mapping=args('sample_mapping'),
-        site_filtering_data=args('site_filtering_data'),
-        vqsr_filtering_data=args('vqsr_filtering_data'),
-        vqsr_tranche_data=args('vqsr_tranche_data'),
-        reference_genome=rg38,
-        final_path=vds_output_path,
-        tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_import_gvs'
-    )
+    import_gvs(args, rg38, vds_path, temp_path)
 
 
-def generate_local_avro_args(avro_prefix, key):
+def local_generate_avro_args(avro_prefix, key):
     def superpartitioned_handler():
         parts = root.split('/')
 
@@ -134,72 +132,41 @@ def regular_handler():
     return ret
 
 
-def import_gvs_local(avro_prefix, tmp_dir, vds_output_path, references_dir):
-    import hail as hl
-
-    unslashed_tmp_dir = tmp_dir if not tmp_dir.endswith('/') else tmp_dir[:-1]
-    hl.init(tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_general')
-
-    references_dir = references_dir[:-1] if references_dir.endswith('/') else references_dir
-    rg38 = hl.get_reference('GRCh38')
-    rg38.add_sequence(f'{references_dir}/Homo_sapiens_assembly38.fasta.gz',
-                      f'{references_dir}/Homo_sapiens_assembly38.fasta.fai')
+def local_import_gvs(avro_path, temp_path, vds_path, references_path):
+    rg38 = init_hail(references_path, temp_path)
 
     def args(key):
-        return generate_local_avro_args(avro_prefix, key)
+        return local_generate_avro_args(avro_path, key)
 
-    hl.import_gvs(
-        vets=args('vets'),
-        refs=args('refs'),
-        sample_mapping=args('sample_mapping'),
-        site_filtering_data=args('site_filtering_data'),
-        vqsr_filtering_data=args('vqsr_filtering_data'),
-        vqsr_tranche_data=args('vqsr_tranche_data'),
-        reference_genome=rg38,
-        final_path=vds_output_path,
-        tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_import_gvs'
-    )
+    import_gvs(args, rg38, vds_path, temp_path)
 
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(allow_abbrev=False,
                                      description='Create base Hail VDS from exported GVS Avro files.')
-    parser.add_argument('--avro-prefix', type=str, help='Prefix under which exported GVS Avro files are found',
-                        default="@AVRO_PREFIX@")
-    parser.add_argument('--write-prefix', type=str,
-                        help='Prefix to which VDS and temporary outputs should be written',
-                        default="@WRITE_PREFIX@")
-    parser.add_argument('--references-dir', type=str,
-                        help='Path to references, only required for local files')
+    parser.add_argument('--avro-path', type=str, help='Path at which exported GVS Avro files are found',
+                        default="@AVRO_PATH")
+    parser.add_argument('--vds-path', type=str, help='Path to which the VDS should be written', default="@VDS_PATH@")
+    parser.add_argument('--temp-path', type=str, help='Path to temporary directory', default="@TEMP_DIR@")
+    parser.add_argument('--references-path', type=str, help='Path to references, only required for local files')
 
     args = parser.parse_args()
 
-    avro_prefix = args.avro_prefix
-    write_prefix = args.write_prefix
-
-    # Remove a trailing slash if present.
-    avro_prefix = avro_prefix if not avro_prefix.endswith('/') else avro_prefix[:-1]
-    write_prefix = write_prefix if not write_prefix.endswith('/') else write_prefix[:-1]
-
-    temp_dir = f"{write_prefix}/temp_hail_gvs_import"
-    vds_output_path = f"{write_prefix}/gvs_export.vds"
-
-    gcs_re = re.compile("^gs://(?P<bucket_name>[^/]+)/(?P<object_prefix>.*)$")
-    match = gcs_re.match(avro_prefix)
-    if match:
-        avro_bucket_name, avro_object_prefix = match.groups()
-        match = gcs_re.match(avro_prefix)
-        if not match:
-            raise ValueError(f"Avro prefix '{write_prefix}' does not look like a GCS path")
-        client = storage.Client()
-        avro_bucket = client.get_bucket(avro_bucket_name)
-        import_gvs_gcs(avro_bucket, avro_object_prefix, vds_output_path, temp_dir)
+    # Remove trailing slashes if present.
+    avro_path, temp_path, vds_path = [p if not p.endswith('/') else p[:-1] for p in
+                                      [args.avro_path, args.temp_path, args.vds_path]]
+
+    is_gcs = [gcs_re.match(p) for p in [avro_path, temp_path, vds_path]]
+    is_not_gcs = [not g for g in is_gcs]
+
+    if all(is_gcs):
+        gcs_import_gvs(avro_path, vds_path, temp_path)
+    elif all(is_not_gcs):
+        references_path = args.references_path
+        if not references_path:
+            raise ValueError(f"--references-path must be specified with local files")
+        if gcs_re.match(references_path):
+            raise ValueError(f"--references-path must refer to a local path")
+        local_import_gvs(avro_path, temp_path, vds_path, references_path)
     else:
-        # assume local filesystem
-        references_dir = args.references_dir
-        if not references_dir:
-            raise ValueError(f"--references-dir must be specified with local files")
-        import_gvs_local(avro_prefix, temp_dir, vds_output_path, references_dir)
-
-    print(f"Hail import temporary path: {temp_dir}")
-    print(f"Final VDS location: {vds_output_path}.")
+        raise ValueError("Arguments appear to be some unsavory mix of GCS and local paths, all or nothing please.")
diff --git a/scripts/variantstore/wdl/extract/test_hail_gvs_import.py b/scripts/variantstore/wdl/extract/test_hail_gvs_import.py
index 359df1101fb..a0602aa9996 100644
--- a/scripts/variantstore/wdl/extract/test_hail_gvs_import.py
+++ b/scripts/variantstore/wdl/extract/test_hail_gvs_import.py
@@ -1,6 +1,6 @@
 import unittest
 
-from hail_gvs_import import generate_gcs_avro_args
+from hail_gvs_import import gcs_generate_avro_args
 from unittest.mock import MagicMock
 
 
@@ -31,7 +31,7 @@ def test_generate_avro_arguments(self):
         bucket = ShamBucket(bucket_name)
         bucket.list_blobs = MagicMock(return_value=blobs)
 
-        actual = generate_gcs_avro_args(
+        actual = gcs_generate_avro_args(
             bucket=bucket,
             blob_prefix=blob_prefix,
             key='sample_mapping'
@@ -54,7 +54,7 @@ def test_generate_avro_arguments(self):
         ]
 
         bucket.list_blobs = MagicMock(return_value=blobs)
-        actual = generate_gcs_avro_args(
+        actual = gcs_generate_avro_args(
             bucket=bucket,
             blob_prefix=blob_prefix,
             key='vets'

From 0b029e3545d009415e217f008a6f848cca3e1b60 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 8 Nov 2022 17:11:32 -0500
Subject: [PATCH 43/49] cleanup

---
 .../wdl/extract/hail_gvs_import.py            | 42 +++++++------------
 1 file changed, 14 insertions(+), 28 deletions(-)

diff --git a/scripts/variantstore/wdl/extract/hail_gvs_import.py b/scripts/variantstore/wdl/extract/hail_gvs_import.py
index 2d9d5f592d7..7bb7d69415c 100644
--- a/scripts/variantstore/wdl/extract/hail_gvs_import.py
+++ b/scripts/variantstore/wdl/extract/hail_gvs_import.py
@@ -22,19 +22,15 @@
 gcs_re = re.compile("^gs://(?P<bucket_name>[^/]+)/(?P<object_prefix>.*)$")
 
 
-def init_hail(references_path, temp_path):
+def import_gvs(argsfn, vds_path, references_path, temp_path):
     import hail as hl
     hl.init(tmp_dir=f'{temp_path}/hail_tmp_general')
 
     rg38 = hl.get_reference('GRCh38')
     rg38.add_sequence(f'{references_path}/Homo_sapiens_assembly38.fasta.gz',
                       f'{references_path}/Homo_sapiens_assembly38.fasta.fai')
-    return rg38
 
 
-def import_gvs(argsfn, rg38, vds_path, temp_path):
-    import hail as hl
-
     hl.import_gvs(
         vets=argsfn('vets'),
         refs=argsfn('refs'),
@@ -96,18 +92,6 @@ def regular_handler(blob_name):
     return ret
 
 
-def gcs_import_gvs(avro_path, vds_path, temp_path):
-    rg38 = init_hail('gs://hail-common/references', temp_path)
-
-    avro_bucket_name, avro_object_prefix = gcs_re.match(avro_path).groups()
-    avro_bucket = storage.Client().get_bucket(avro_bucket_name)
-
-    def args(key):
-        return gcs_generate_avro_args(avro_bucket, avro_object_prefix, key)
-
-    import_gvs(args, rg38, vds_path, temp_path)
-
-
 def local_generate_avro_args(avro_prefix, key):
     def superpartitioned_handler():
         parts = root.split('/')
@@ -132,15 +116,6 @@ def regular_handler():
     return ret
 
 
-def local_import_gvs(avro_path, temp_path, vds_path, references_path):
-    rg38 = init_hail(references_path, temp_path)
-
-    def args(key):
-        return local_generate_avro_args(avro_path, key)
-
-    import_gvs(args, rg38, vds_path, temp_path)
-
-
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(allow_abbrev=False,
                                      description='Create base Hail VDS from exported GVS Avro files.')
@@ -160,13 +135,24 @@ def args(key):
     is_not_gcs = [not g for g in is_gcs]
 
     if all(is_gcs):
-        gcs_import_gvs(avro_path, vds_path, temp_path)
+        avro_bucket_name, avro_object_prefix = gcs_re.match(avro_path).groups()
+        avro_bucket = storage.Client().get_bucket(avro_bucket_name)
+
+        def args(key):
+            return gcs_generate_avro_args(avro_bucket, avro_object_prefix, key)
+
+        import_gvs(args, vds_path, 'gs://hail-common/references', temp_path)
+
     elif all(is_not_gcs):
         references_path = args.references_path
         if not references_path:
             raise ValueError(f"--references-path must be specified with local files")
         if gcs_re.match(references_path):
             raise ValueError(f"--references-path must refer to a local path")
-        local_import_gvs(avro_path, temp_path, vds_path, references_path)
+
+        def args(key):
+            return local_generate_avro_args(avro_path, key)
+
+        import_gvs(args, vds_path, references_path, temp_path)
     else:
         raise ValueError("Arguments appear to be some unsavory mix of GCS and local paths, all or nothing please.")

From ba03a9fdf5da03e3035a263082d002673a06407e Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Tue, 8 Nov 2022 17:42:17 -0500
Subject: [PATCH 44/49] cleanup, update references

---
 scripts/variantstore/wdl/GvsAssignIds.wdl     |  4 ++--
 .../variantstore/wdl/GvsCallsetStatistics.wdl | 10 +++++-----
 .../wdl/GvsExtractAvroFilesForHail.wdl        |  6 +++---
 .../variantstore/wdl/GvsExtractCallset.wdl    |  6 +++---
 scripts/variantstore/wdl/GvsImportGenomes.wdl |  6 +++---
 .../variantstore/wdl/GvsPopulateAltAllele.wdl |  6 +++---
 .../wdl/GvsQuickstartHailIntegration.wdl      | 19 ++++++++++++-------
 scripts/variantstore/wdl/GvsUtils.wdl         | 12 ++++++------
 .../wdl/extract/hail_gvs_import.py            | 12 ++++++++----
 9 files changed, 45 insertions(+), 36 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsAssignIds.wdl b/scripts/variantstore/wdl/GvsAssignIds.wdl
index 80dfe2f22db..883b6cab32f 100644
--- a/scripts/variantstore/wdl/GvsAssignIds.wdl
+++ b/scripts/variantstore/wdl/GvsAssignIds.wdl
@@ -146,7 +146,7 @@ task AssignIds {
     bq --project_id=~{project_id} rm -f -t ~{dataset_name}.sample_id_assignment_lock
   >>>
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3.75 GB"
     disks: "local-disk " + 10 + " HDD"
     cpu: 1
@@ -196,7 +196,7 @@ task CreateCostObservabilityTable {
     fi
   >>>
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
   }
   output {
     Boolean done = true
diff --git a/scripts/variantstore/wdl/GvsCallsetStatistics.wdl b/scripts/variantstore/wdl/GvsCallsetStatistics.wdl
index 85fd890354a..b7ac4a29a14 100644
--- a/scripts/variantstore/wdl/GvsCallsetStatistics.wdl
+++ b/scripts/variantstore/wdl/GvsCallsetStatistics.wdl
@@ -266,7 +266,7 @@ task CreateTables {
         fi
     >>>
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
     output {
@@ -400,7 +400,7 @@ task CollectMetricsForChromosome {
         Boolean done = true
     }
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
 }
@@ -471,7 +471,7 @@ task AggregateMetricsAcrossChromosomes {
         Boolean done = true
     }
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
 }
@@ -543,7 +543,7 @@ task CollectStatistics {
         Boolean done = true
     }
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
 }
@@ -572,7 +572,7 @@ task ExportToCSV {
         File callset_statistics = "~{statistics_table}.csv"
     }
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
 }
diff --git a/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl b/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
index 4bba71c214e..e608f69fd2d 100644
--- a/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
+++ b/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
@@ -82,7 +82,7 @@ task OutputPath {
         File out = stdout()
     }
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
 }
@@ -153,7 +153,7 @@ task ExtractFromNonSuperpartitionedTables {
     }
 
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
 }
@@ -220,7 +220,7 @@ task ExtractFromSuperpartitionedTables {
     }
 
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
 }
diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl
index cf6e4143ada..c354ab16f14 100644
--- a/scripts/variantstore/wdl/GvsExtractCallset.wdl
+++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl
@@ -355,7 +355,7 @@ task SumBytes {
     print(total_mb);"
   >>>
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 500 HDD"
     preemptible: 3
@@ -394,7 +394,7 @@ task CreateManifest {
   }
 
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 500 HDD"
     preemptible: 3
@@ -436,7 +436,7 @@ task GenerateSampleListFile {
   }
 
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 500 HDD"
     preemptible: 3
diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl
index bcc0ce5954a..bfce3aeff60 100644
--- a/scripts/variantstore/wdl/GvsImportGenomes.wdl
+++ b/scripts/variantstore/wdl/GvsImportGenomes.wdl
@@ -143,7 +143,7 @@ task CreateFOFNs {
   >>>
   # Can't use alpine version here because their version of split does not recognize the -d option
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     bootDiskSizeGb: 15
     memory: "3 GB"
     disks: "local-disk 10 HDD"
@@ -293,7 +293,7 @@ task SetIsLoadedColumn {
                      AND sls2.status = "FINISHED")'
   >>>
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "1 GB"
     disks: "local-disk 10 HDD"
     cpu: 1
@@ -382,7 +382,7 @@ task GetUningestedSampleIds {
     bq --project_id=~{project_id} rm -f=true ~{temp_table}
   >>>
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "1 GB"
     disks: "local-disk 10 HDD"
     preemptible: 5
diff --git a/scripts/variantstore/wdl/GvsPopulateAltAllele.wdl b/scripts/variantstore/wdl/GvsPopulateAltAllele.wdl
index 3929a892990..9b5e61e4d96 100644
--- a/scripts/variantstore/wdl/GvsPopulateAltAllele.wdl
+++ b/scripts/variantstore/wdl/GvsPopulateAltAllele.wdl
@@ -86,7 +86,7 @@ task GetMaxSampleId {
   }
 
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     preemptible: 3
@@ -138,7 +138,7 @@ task GetVetTableNames {
     split -l $num_tables_per_file vet_tables.csv vet_tables_
   >>>
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     preemptible: 3
@@ -199,7 +199,7 @@ task CreateAltAlleleTable {
 
   >>>
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     cpu: 1
diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 27e7f6bde2b..230cd161efd 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -96,8 +96,8 @@ task CreateAndTieOutVds {
         # `avro_prefix` includes a trailing `avro` so don't add another `avro` here.
         gcloud storage cp --recursive ~{avro_prefix} $PWD
 
-        export REFERENCES=$PWD/references
-        mkdir -p ${REFERENCES}
+        export REFERENCES_PATH=$PWD/references
+        mkdir -p ${REFERENCES_PATH}
 
         gcloud storage cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta*' ${REFERENCES}
 
@@ -113,13 +113,18 @@ task CreateAndTieOutVds {
 
         export WORK=$PWD/work
         mkdir ${WORK}
-        export AVRO=$PWD/avro
-        python3 ./hail_gvs_import.py --avro-prefix ${AVRO} --write-prefix ${WORK} --references-dir ${REFERENCES}
 
-        export LOCAL_VDS_PATH=${WORK}/gvs_export.vds
+        export TEMP_PATH=$WORK/temp
+        mkdir ${TEMP_PATH}
+
+        export VDS_PATH=$WORK/gvs_import.vds
+        export AVRO_PATH=$PWD/avro
+
+        python3 ./hail_gvs_import.py --avro-path ${AVRO_PATH} --vds-path ${VDS_PATH} --temp-path ${TEMP_PATH} --references-path ${REFERENCES_PATH}
+
         export JOINED_MATRIX_TABLE_PATH=${WORK}/joined.mt
 
-        python3 ./hail_join_vds_vcfs.py --vds-path ${LOCAL_VDS_PATH} --joined-matrix-table-path ${JOINED_MATRIX_TABLE_PATH} *.vcf.gz
+        python3 ./hail_join_vds_vcfs.py --vds-path ${VDS_PATH} --joined-matrix-table-path ${JOINED_MATRIX_TABLE_PATH} *.vcf.gz
 
         # Copy up the VDS
         gcloud storage cp --recursive ${LOCAL_VDS_PATH} ~{vds_destination_path}
@@ -130,7 +135,7 @@ task CreateAndTieOutVds {
     >>>
     runtime {
         # `slim` here to be able to use Java
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-slim"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-slim"
         disks: "local-disk 2000 HDD"
         memory: "30 GiB"
     }
diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl
index 07aaf7c89df..5e5ea249c83 100644
--- a/scripts/variantstore/wdl/GvsUtils.wdl
+++ b/scripts/variantstore/wdl/GvsUtils.wdl
@@ -164,7 +164,7 @@ task GetBQTableLastModifiedDatetime {
   }
 
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     preemptible: 3
@@ -202,7 +202,7 @@ task GetBQTablesMaxLastModifiedTimestamp {
   }
 
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     preemptible: 3
@@ -284,7 +284,7 @@ task BuildGATKJarAndCreateDataset {
   }
 
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-slim"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-slim"
     disks: "local-disk 500 HDD"
   }
 }
@@ -387,7 +387,7 @@ task GetNumSamplesLoaded {
   }
 
   runtime {
-    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     preemptible: 3
@@ -415,7 +415,7 @@ task CountSuperpartitions {
         ' | sed 1d > num_superpartitions.txt
     >>>
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         disks: "local-disk 500 HDD"
     }
     output {
@@ -460,7 +460,7 @@ task ValidateFilterSetName {
     }
 
     runtime {
-        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine"
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
         memory: "3 GB"
         disks: "local-disk 500 HDD"
         preemptible: 3
diff --git a/scripts/variantstore/wdl/extract/hail_gvs_import.py b/scripts/variantstore/wdl/extract/hail_gvs_import.py
index 7bb7d69415c..86c9271e0e2 100644
--- a/scripts/variantstore/wdl/extract/hail_gvs_import.py
+++ b/scripts/variantstore/wdl/extract/hail_gvs_import.py
@@ -120,10 +120,14 @@ def regular_handler():
     parser = argparse.ArgumentParser(allow_abbrev=False,
                                      description='Create base Hail VDS from exported GVS Avro files.')
     parser.add_argument('--avro-path', type=str, help='Path at which exported GVS Avro files are found',
-                        default="@AVRO_PATH")
-    parser.add_argument('--vds-path', type=str, help='Path to which the VDS should be written', default="@VDS_PATH@")
-    parser.add_argument('--temp-path', type=str, help='Path to temporary directory', default="@TEMP_DIR@")
-    parser.add_argument('--references-path', type=str, help='Path to references, only required for local files')
+                        default="@AVRO_PATH@",
+                        required=True)
+    parser.add_argument('--vds-path', type=str, help='Path to which the VDS should be written', default="@VDS_PATH@",
+                        required=True)
+    parser.add_argument('--temp-path', type=str, help='Path to temporary directory', default="@TEMP_DIR@",
+                        required=True)
+    parser.add_argument('--references-path', type=str, help='Path to references, only required for local files',
+                        required=False)
 
     args = parser.parse_args()
 

From f8a4bb5c398742f746ecbdeec6c4e44bc88ceb83 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Wed, 9 Nov 2022 01:23:06 -0500
Subject: [PATCH 45/49] oops

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 230cd161efd..20a8c451360 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -99,7 +99,7 @@ task CreateAndTieOutVds {
         export REFERENCES_PATH=$PWD/references
         mkdir -p ${REFERENCES_PATH}
 
-        gcloud storage cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta*' ${REFERENCES}
+        gcloud storage cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta*' ${REFERENCES_PATH}
 
         # Temurin Java 8
         apt-get -qq install wget apt-transport-https gnupg

From ed64917b217190469635ea2392a2b88b81654377 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Wed, 9 Nov 2022 05:32:11 -0500
Subject: [PATCH 46/49] omg

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 20a8c451360..78694b9f90d 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -127,7 +127,7 @@ task CreateAndTieOutVds {
         python3 ./hail_join_vds_vcfs.py --vds-path ${VDS_PATH} --joined-matrix-table-path ${JOINED_MATRIX_TABLE_PATH} *.vcf.gz
 
         # Copy up the VDS
-        gcloud storage cp --recursive ${LOCAL_VDS_PATH} ~{vds_destination_path}
+        gcloud storage cp --recursive ${VDS_PATH} ~{vds_destination_path}
 
         pip install pytest
         ln -s ${WORK}/joined.mt .

From 308c7034fc9717186ba88bdd3ce4ced3b1341185 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Wed, 9 Nov 2022 12:58:15 -0500
Subject: [PATCH 47/49] comment my trickery

---
 scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
index 78694b9f90d..c3f89714e2c 100644
--- a/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+++ b/scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
@@ -72,8 +72,8 @@ task CreateAndTieOutVds {
         PS4='\D{+%F %T} \w $ '
         set -o errexit -o nounset -o pipefail -o xtrace
 
+        # Copy the versions of the Hail import and tieout scripts for this branch from GitHub.
         script_url_prefix="https://raw.githubusercontent.com/broadinstitute/gatk/~{branch_name}/scripts/variantstore/wdl/extract"
-
         for script in hail_gvs_import.py hail_join_vds_vcfs.py gvs_vds_tie_out.py
         do
             curl --silent --location --remote-name "${script_url_prefix}/${script}"

From b42d7b1cae029fe649e230d14f8e52149e7c4aab Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 10 Nov 2022 15:21:13 -0500
Subject: [PATCH 48/49] delete erroneous comment

---
 scripts/variantstore/wdl/GvsImportGenomes.wdl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl
index bfce3aeff60..ffef0ec88ef 100644
--- a/scripts/variantstore/wdl/GvsImportGenomes.wdl
+++ b/scripts/variantstore/wdl/GvsImportGenomes.wdl
@@ -141,7 +141,6 @@ task CreateFOFNs {
     split -a 5 -l ~{batch_size} ~{input_vcf_index_list} batched_vcf_indexes.
     split -a 5 -l ~{batch_size} ~{sample_name_list} batched_sample_names.
   >>>
-  # Can't use alpine version here because their version of split does not recognize the -d option
   runtime {
     docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:409.0.0-alpine"
     bootDiskSizeGb: 15

From bd65357246accdc767bade0c6a7449c7c916bb6a Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@broadinstitute.org>
Date: Thu, 10 Nov 2022 15:45:12 -0500
Subject: [PATCH 49/49] remove junk

---
 scripts/variantstore/wdl/extract/gvs_vds_tie_out.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
index 4bc774a38a3..40765c0ff04 100644
--- a/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
+++ b/scripts/variantstore/wdl/extract/gvs_vds_tie_out.py
@@ -1,5 +1,3 @@
-# gvs_vds_tie_out.py
-
 import hail as hl
 import pytest