Cleanup scripts/variantstore [VS-414]

.dockstore.yml

@@ -110,17 +110,13 @@ workflows:
    - name: GvsExtractCallset
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCallset.wdl
-     testParameterFiles:
-       - /scripts/variantstore/wdl/GvsExtractCallset.example.inputs.json
      filters:
        branches:
          - master
          - ah_var_store
    - name: GvsImportGenomes
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsImportGenomes.wdl
-     testParameterFiles:
-       - /scripts/variantstore/wdl/GvsImportGenomes.example.inputs.json
      filters:
        branches:
          - master
@@ -137,8 +133,6 @@ workflows:
    - name: GvsCreateVAT
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateVAT.wdl
-     testParameterFiles:
-       - /scripts/variantstore/wdl/GvsCreateVAT.example.inputs.json
      filters:
        branches:
          - master

scripts/variantstore/AOU_GVS_WORKSPACE.md

@@ -153,4 +153,4 @@ TODO:
 
 ## 5. Your VCF is ready!!
 
-The sharded VCF outut files are listed in the `ExtractTask.output_vcf` workflow output, and the associated index files are listed in `ExtractTask.output_vcf_index`
+The sharded VCF output files are listed in the `ExtractTask.output_vcf` workflow output, and the associated index files are listed in `ExtractTask.output_vcf_index`

scripts/variantstore/variant_annotations_table/README.md

@@ -12,14 +12,14 @@ The pipeline takes in a jointVCF and outputs a table in BigQuery.
 
 ### Run GvsCreateVAT:
 
-Most of the inputs are constants — like the reference, or a table schema — and dont require any additional work (and paths can be found in the [example inputs json](/scripts/variantstore/wdl/GvsCreateVAT.example.inputs.json)). However for the specific data being put in the VAT, three inputs need to be created.
+Most of the inputs are constants — like the reference, or a table schema — and don't require any additional work, or have defaults set in the WDL). However for the specific data being put in the VAT, three inputs need to be created.
 
 The first two of these inputs are two files — one of the file/vcf/shards you want to use for the VAT, and their corresponding index files. These are labelled as `inputFileofFileNames` and `inputFileofIndexFileNames` and need to be copied into a GCP bucket that this pipeline will have access to (eg. this bucket: `gs://aou-genomics-curation-prod-processing/vat/`) for easy access during the workflow.
 The third input is the ancestry file from the ancestry pipeline which will be used to calculate AC, AN and AF for all subpopulations. It needs to be copied into a GCP bucket that this pipeline will have access to. This input has been labelled as the `ancestry_file`.
 
 Most of the other files are specific to where the VAT will live, like the project_id and dataset_name and the table_suffix which will name the VAT itself as vat_`table_suffix` as well as a GCP bucket location, the output_path, for the intermediary files and the VAT export in tsv form.
 
-The provided [example inputs json](/scripts/variantstore/wdl/GvsCreateVAT.example.inputs.json) indicates all of the inputs.
+All optional inputs are provided with default values.
 
 
 ### Notes:

scripts/variantstore/wdl/WDL_TESTING.md

@@ -2,7 +2,7 @@
 
 Some data (including All of Us data) will be processed using a service account (SA) that has access to the relevant data (GCP storage) and BigQuery (BQ) resources.
 
-Our WLDs are written so that they can be run EITHER (1) as the user (no `service_account_json` file provided as input) OR (2) as the SA (by providing a `service_account_json` input file to the WDL).
+Our WDLs are written so that they can be run EITHER (1) as the user (no `service_account_json` file provided as input) OR (2) as the SA (by providing a `service_account_json` input file to the WDL).
 
 ## Manual steps to create testing resources
 To test running WDLs using a SA, we have created a project, SA, buckets, and BQ datasets that mirror the permissions in the AoU setup. These include: