318 Sites only filtered vcf then annotate wdl

.dockstore.yml

@@ -93,6 +93,14 @@ workflows:
        branches:
          - master
          - ah_var_store
+   - name: GvsSitesOnlyVCF
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl
+     testParameterFiles:
+       - /scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json
+     filters:
+       branches:
+         - ah_var_store
    - name: MitochondriaPipeline
      subclass: WDL
      primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl

scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json

@@ -0,0 +1,14 @@
+{
+  "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz"],
+  "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcf_indices": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz.tbi", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz.tbi"],
+  "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only",
+  "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate",
+  "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz",
+  "GvsSitesOnlyVCF.vat_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vat_schema.json",
+  "GvsSitesOnlyVCF.variant_transcript_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vt_schema.json",
+  "GvsSitesOnlyVCF.genes_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/genes_schema.json",
+  "GvsSitesOnlyVCF.output_path": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jul13/",
+  "GvsSitesOnlyVCF.table_suffix": "jul13",
+  "GvsSitesOnlyVCF.project_id": "spec-ops-aou",
+  "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing"
+}