Public Terra workspaces are a useful way to share data and results as part of the publication process. This article describes how peers can cite individual workflows and workspaces in their own work, as well as the versions of the Cromwell execution engine and the Workflow Description Language (WDL) used in your analysis on Terra.
Who can see your Terra workspace? You can share your workflow and workspace with any reviewer who has a Terra account. Once you are ready to publish your work, you can change the workspace permission to include individuals or groups with Terra access, or reach out to our support team to help make the workspace publicly readable. You can also consider featuring your workspace to make it easy for others to reproduce your analysis.
Anyone can see the dashboard of a featured workspace, even if they do not have an account on Terra.
Citing workflows and workspaces
You can cite an individual workflow or an entire workspace (workflows, Jupyter Notebooks, test data, dashboard info, etc.) as demonstrated below.
Citation format
Last Name, First Initial. (Year, Month, Day that the workspace/method was last modified) name of your workspace/method [workspace or method] Retrieved Date from URL to workspace/method/method results
Citation example (workspace)
Kovalsky, A. (2020, January 1) Somatic-CNVs-GATK4 copy_akovalsk 10_31_2019 [workspace] Retrieved October 31, 2019, https://app.terra.bio/#workspaces/help-gatk/Somatic-CNVs-GATK4%20copy_akovalsk%2010_31_2019
Citation example (workflow)
Shifaw, B. (2021, April 21) gatk/2-CNV_Somatic_Pair (Version 4.2.0.0) [Workflow] Retrieved April 22, 2021 from https://app.terra.bio/#workspaces/help-gatk/Somatic-CNVs-GATK4/workflows/help-gatk/2-CNV_Somatic_Pair
Where to find citation information
The citation information can be found in the workspace dashboard. In some instances, the original authors may include a section detailing all the people involved in the creation of the workspace. If that doesn't exist, use the owner's email listed on the right-hand panel of the Dashboard tab to contact the owners about the authors of the workspace. The right-hand panel also lists the date the workspace was last modified which can be used directly in your citation.
Make your workflows more citable with Dockstore Dockstore supports researchers who want to publish citable workflows in different ways, such as creating snapshots and requesting DOIs. Researchers can become verified users and link their ORCID profiles to their Dockstore account, as described in this blog post.
Citing Cromwell/WDL
You might also want to cite the Cromwell execution engine or the Workflow Development Language (WDL) - for example, when publishing analyses using one of the Broad Institute's workflows. Follow the example below to cite Cromwell or WDL:
Voss K, Gentry J and Van der Auwera G.
Full-stack genomics pipelining with GATK4 + WDL + Cromwell [version 1; not peer reviewed].
F1000Research 2017, 6(ISCB Comm J):1379 (poster)
(doi: 10.7490/f1000research.1114631.1)
Citing the Terra platform
If you are simply looking for a way to cite the Terra platform as a whole, please cite the landing page as you would any website. We plan to write a manuscript about Terra; once that is published or posted as a pre-print, we will update this article with full citation information.