Many Tools and workflows already exist in Terra to help carry out different steps in your research journey. Below is a step-by-step outline for finding Tools in the Broad Methods Repository.
Note that FireCloud "Methods" are called "Tools" in Terra
1. Click on Code and Tools in the drop down menu from the three horizontal bars at top left in any page in Terra:
2. This will direct you to to the Terra Tools library, which features GATK4 Best Practices workflows front and center:
3. If the Tool/workflow you need is not there, you can find additional workflows in Dockstore or the Broad Methods Repository by selecting one of these options in the menu on the right side of the page:
4. The Broad Methods Repository button will take you to the legacy Methods repository, where you can browse and search public and Featured methods:
4. To export the Tool or for more information, click on the Tool name (a link in the "Method" column). You will be taken to the Tool page, which will include a summary description and configuration and snapshot options (if available). You can export the Tool to your workspace by clicking the Export button (arrow at right in the screenshot) or clone by selecting the "Clone" button (circled at left in the screenshot below) :
A copy of the workflow will now be in the Tools tab of your workspace, ready for you to use for batch analysis!