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@rsasch
rsasch committed May 8, 2024
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Expand Up @@ -64,17 +64,17 @@ The [GVS beta workspace](https://app.terra.bio/#workspaces/gvs-prod/Genomic_Vari

The table below describes the GVS workflow input variables:

| Input variable name | Description | Type |
|------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------|
| dataset_name | Name of the BigQuery dataset used to hold input samples, filtering model data, and other tables created during the workflow. | String |
| project_id | Name of the Google project that contains the BigQuery dataset. | String |
| Input variable name | Description | Type |
|------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------|
| dataset_name | Name of the BigQuery dataset used to hold input samples, filtering model data, and other tables created during the workflow. | String |
| project_id | Name of the Google project that contains the BigQuery dataset. | String |
| call_set_identifier | Used to name the filter model, BigQuery extract tables, and final joint VCF shards; should begin with a letter; valid characters include A-z, 0-9, “.”, “,”, “-”, and “_”. | String |
| extract_output_gcs_dir | The GCS path where the callset VCFs, VCF indexes and interval lists will be copied. |
| sample_id_column_name | The column in the workspace Data tab that contains a unique identifier for each sample (the workflow will fail if there are any duplicates). | String |
| vcf_files_column_name | The column in the workspace Data tab that contains the path to the VCF file for each sample. | String |
| vcf_index_files_column_name | The column in the workspace Data tab that contains the path to the VCF index file for each sample. | String |
| use_classic_VQSR | Optional; defaults to false since September 1, 2023. | Boolean |
| billing_project_id | Optional; Google project ID to charge for the egress of the GVCFs and index files, useful if the bucket the GVCFs are in has "requester pays" enabled | String |
| extract_output_gcs_dir | The GCS path where the callset VCFs, VCF indexes, interval lists, and manifest will be copied. |
| sample_id_column_name | The column in the workspace Data tab that contains a unique identifier for each sample (the workflow will fail if there are any duplicates). | String |
| vcf_files_column_name | The column in the workspace Data tab that contains the path to the VCF file for each sample. | String |
| vcf_index_files_column_name | The column in the workspace Data tab that contains the path to the VCF index file for each sample. | String |
| use_classic_VQSR | Optional; defaults to false since September 1, 2023. | Boolean |
| billing_project_id | Optional; Google project ID to charge for the egress of the GVCFs and index files, useful if the bucket the GVCFs are in has "requester pays" enabled | String |

## Tasks and tools

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