Run GVS on Verily Workbench

Prior reading: Workflows overview

Purpose: This document provides a tutorial for running GVS in Verily Workbench.

Introduction

Genomic Variant Store (GVS) is a WDL-based workflow developed by the Broad Institute. This tutorial shows you how to run GVS in your own workspace.

Step-by-step instructions

1. Create a Cloud Storage bucket to hold WDL files

Workbench currently requires that the WDL file(s) for your workflow is in a bucket. For this example, we create a new bucket.

1. In the Resources tab, click + New resource and then New Cloud Storage bucket.
2. Create a name for the bucket. In this example, we'll name it workflows_bucket. Click Create bucket.

2. Create a BigQuery dataset

The GVS workflow requires a BigQuery dataset to exist that it can read and write to. For this example, we'll create a new BigQuery dataset.

1. In Resources, click + New resource and then New BigQuery dataset.
2. Create a name for the dataset. In this example, we'll name it gvs_1. Click Create dataset.

3. Get the WDLs into the bucket

The WDLs used are available on GitHub here. To add them to the workflows_bucket created in step 1, run:

git clone https://github.com/verily-src/workbench-examples.git .
cd workbench-examples/cromwell_setup/gvs_wdls/known_good_wdls
gsutil cp *.wdl $BUCKET_NAME

4. Add the workflow

Navigate to the Workflows tab and click + Add workflow (or Add your first workflow if you haven't created any workflows yet). Add the WDL named GvsJointVariantCalling.wdl.

5. Create a new job

Click on the + New job button. Navigate to the next Prepare inputs page.

6. Enter the inputs

Enter in the following values:

7. Monitor the workflow

In the Workflows tab, click the Job status sub-tab to monitor jobs as they run and complete.

8. Get outputs

Once the workflow completes, browse the workspace bucket and navigate to the task containing the sharded VCF outputs.