Terra

Terra is a fully managed bioinformatics platform powered by the Google Cloud Platform and Cromwell. It natively supports workflows in the WDL format. Below demonstrates how to run the 02_download_collection_files.wdl workflow via Terra. This workflow should take between 5-10 minutes to run.

Prerequisites

Before beginning, ensure you have the following:

• A Valid Google Account

• A Valid Google Cloud Platform Account (Free accounts available with $300 in free compute for a 90 day trial period)

• Terra Account

• (Optional) git

See getting started for a guide on how to link your GCP account and billing information to Terra Bio.

Getting Started

Download the worked examples repository containing the necessary workflow file 02_download_collection_files.wdl, by one of the following methods.

1. Clone with Git

git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git

or

2. Download and Unzip

Create a workspace that will house the workflow and output files. A cloud environment is not needed to run WDL workflows and can be skipped when prompted. [block:image] { "images": [ { " image": [ "https://files.readme.io/e6eacb1-create-workspace1.gif", "create-workspace1.gif", 1920, 969, "#000000" ], " border": true, "sizing": "full" } ] } [/block]

Importing a workflow

• Step 1: Once your project has been setup, import the WDL workflow 02_download_collection_files.wdl to Terra by navigating to "Workflows", and selecting "Find a Workflow".

Common workflows can be obtained from Dockstore, or the Broad Institute. To import a custom workflow, select the "Broad Methods Repository" and log in using your Google account.

new-workflow1.gif

• Step 2: Select "Create New Method", and upload 02_download_collection_files.wdl or copy and paste its contents.

• Step 3: Next, export the newly created workflow to your Terra workspace by selecting Export to Workspace, and Use Blank Configuration.

new-workflow2.gif

Running a workflow

• Step 1: Return to your Terra workspace, and select the newly created workflow. By default, Terra workflows are set to output to data tables.

• Step 2: Select "Run workflow with inputs defined by file paths" and click "Run Analysis" to start the workflow. Optionally, custom inputs can be specified.

new-workflow3.gif

• Step 3: Job progress can be monitored in the "Job History" tab.

job-history1.png

• Step 4: Once completed, the outputted files can be found in the "Data" tab under Files. Downloading files from Terra ( Google Cloud Bucket) will incur a fee depending on the size.

download-file1.gif