Get started running workflows

We think the best way to get started running workflows on Terra is to dive in and get started! The Terra QuickStart workspace is a hands-on practice that guides you through the process. You'll follow the steps below to get experience with increasi...
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Getting started with GATK workflows in the cloud FAQs

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 (and its JSON) in the Methods Repository

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 FireCloud "methods" are called "workflows" in Terra...
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Importing a workflow and its configuration file from Dockstore into Terra

Overview Dockstore is a GA4GH-compliant, open-source platform for sharing Docker-based tools, such as Terra-compatible workflows written in the Worflow Description Language (WDL).  This tutorial covers how to: Access and select a Dockstore workfl...
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What happens when you launch a workflow?

What is going on behind-the-curtain when a you hit "Launch Analysis" from the Terra UI? This article helps you understand the components working in the backend - like what Cromwell does versus what Google Pipelines API does - to help understand wh...
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How to set up a workflow analysis

This article explains how to set up (configure) your workflow analysis in the Terra UI. Note that this article is intended primarily for analyses using data from the workspace data table. Differences for using direct paths are noted in "hints" box...
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Getting workflows up and running faster with a JSON file

Configuring with a JSON file helps avoid manually typing in workflow inputs and outputs and can get your WDL up and running in record time. This is especially useful when you want to quickly test that a WDL workflow can run successfully on Terra w...
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How much does my workflow cost?

Executing jobs on the cloud can be a little scary if you don't know how much you're spending. For peace of mind that you're not going over a project budget, read on for two ways to understand the cost of an executed workflow. Option 1: Terra's bui...
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Monitor and troubleshoot in the Job History tab

The Job History tab is your workspace operations dashboard, where you can check the status of past and current workflow submissions, drill down to see what’s going on and find direct links to all input and output files involved. This article walks...
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Scaling your workflow submissions

The full power of working in the cloud is realized in your ability to scale. Many users today are already taking advantage of Terra and Google Cloud to submit workflows large in size and in number. Whether you are new to working in the cloud or yo...
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Create, edit, and share a new workflow

Creating or editing a new Workflow in Terra currently requires working in the "Broad Methods Repository." This article includes step-by step instructions for how to 1. Create a new workflow2. Edit a workflow3. Share or clone a workflow as well as ...
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Creating a list file of reads for input to a workflow

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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Out of Memory Retry

Learn how to configure your workflow to immediately retry certain tasks if the only error was to run out of memory. Contents - How to enable memory retry- Make sure your task is "more-memory" aware (compatible)- How memory retry works (technical d...
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How to test workflows locally

When creating WDL workflows, you can test on a local installation of the Cromwell execution engine prior to uploading and testing in Terra. Cromwell is the workflow execution service used to run and test WDL workflows. Cromwell is a Java applicati...
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Managing data and automating workflows with the FISS API

FireCloud Service Selector (FISS) is a utility command module that allows API (Application Programming Interface) calls from the notebook to the workspace. Scripting with FISS is much like you would run on a local machine, but with Terra's built-i...
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Deeper dive - WDLs, workflows, and tasks

Identifying workflow and task inputs and outputs Inputs and outputs are defined in the WDL.and can be at the "workflow" or the "task" level. Terra interprets the WDL and provides an input "form" to fill out. The outputs part of the form is optiona...
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Accessing archived workflow details

To improve performance, Terra archives some workflow details (metadata) after a year. Read on to understand what workflow-level details are archived and how to retrieve them if you need them.  Contents - Archiving workflow details FAQs- How to acc...
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