Run GVS on Verily Workbench

Prior reading: Workflows in Verily Workbench: Cromwell, dsub, and Nextflow

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 GCS 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 resources tab, click “+ Cloud resource” -> “New Cloud Storage bucket”
2. Give it a name and click “Create bucket”. In this example I name it workflows_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 create a new BQ dataset.

1. In resources tab, click “+ Cloud resource” -> “New BigQuery dataset”
2. Give it a name and click “Create dataset”. In this example I name it gvs_1:

3 Get the WDLs into the bucket

The WDLs used are available on github here. To get them into the bucket from step 1, run:

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

4 Add the Workflow

Navigate to the Workflows section and click “+Add workflow”. 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, there is a section to monitor the 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.