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Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate.
Terra powers important scientific projects like FireCloud, AnVIL, DataSTAGE. Learn more.

Terra uses pipelines in Workflow Description Language (WDLs) for batch processing genomics data. Find here documentation on setting up and running WDLS using sample or your own data in a Google Cloud bucket.

  • Getting started with GATK workflows in the cloud FAQs plus-icon minus-icon

    If you're new to running GATK on a cloud-based platform, or new to Terra, this information will help get you started. From pre-processing raw sequencing data through variant calling and joint calling, showcase workspaces provide fully reproducible...
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  • Finding the workflow (method) you need in the Methods Repository plus-icon minus-icon

    Many workflows already exist in Terra to help carry out different steps in your research journey. Below is a step-by-step outline for finding workflows in the Broad Methods Repository.   =================================================  Note that...
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  • Configure a workflow to process your data plus-icon minus-icon

    Configuring a workflow to run on your data means defining or customizing the parameters the WDL needs to run. These include Inputs - such as reference files, compute parameters, and input data file names and locations - and Outputs. Some workflows...
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  • Creating a list file of reads for input to a workflow plus-icon minus-icon

    Raw genomics data is in the form of many reads from the sequencer. Since it would be messy and time consuming to type in the location of every one of these data files as input for a WDL, the input is often a 'list' file. This file is just a list o...
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  • Troubleshooting errors in Job Manager plus-icon minus-icon

    Workflows can fail for a lot of different reasons. If you're lucky, you just have the wrong inputs plugged into the configuration, which is typically fast to fail and fast to fix. More complex are errors in the workflow code: bugs, or limitations ...
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  • CPUs and persistent disk quotas: What are they and how do you request more? plus-icon minus-icon

      In the Google Cloud Platform (GCP), quotas specify how many resources, such as central processing units (CPUs) and persistent disks (PDs), can be used by a Google Project at any given time. Quotas prevent unforeseen spikes in usage so resources ...
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  • Updating workflows to the Latest Version plus-icon minus-icon

    This article shows how to add a new version of a workflow to your Terra workspace in two instances - workflows hosted on Dockstore and those in the Broad Methods Repository.  Note for FireCloud users: you may be familiar with the "snapshots" creat...
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  • Create and/or edit a new workflow plus-icon minus-icon

    In order to Create a new Workflow in Terra, the process requires working through the "Broad Methods Repository". Follow the steps below to Create a new Workflow and how to edit a workflow. A. Create a new Workflow 1. From your Terra workspace, na...
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