One exciting Terra feature is the ability to share workspaces as part of the publication process. Publications and pre-prints can refer reviewers and/or peers to Terra-based resources, providing a simple route for researchers to explore each other's methodologies in detail. This article describes the format for citing individual workflows and workspaces, as well as the versions of the Cromwell execution engine and the Workflow Description Language (WDL) used on the Terra platform.
Remember that you can also share the 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 think about featuring your workspace to make it easy for others to reproduce your analysis.
Citing workflows and workspaces
Citing a workspace or workflow can facilitate the examination of your data by reviewers. You can cite either 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 your workspace/method was last modified) name of your workspace/method [workspace or method] Retrieved Date from URL to workspace/method/method results
Citation example (workspaces): 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 (workflows): Shifaw, B. (2021, April 21) gatk/2-CNV_Somatic_Pair (Version 18.104.22.168) [Workflow] Retrieved April 22, 2021 from https://app.terra.bio/#workspaces/help-gatk/Somatic-CNVs-GATK4/workflows/help-gatk/2-CNV_Somatic_Pair
The citation info for a workspace can be obtained from the dashboard. In some instances, the original authors may have a section in the dashboard markdown 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 and get 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.
Dockstore also supports researchers who want to publish citable workflows in a number of ways, such as creating snapshots and requesting DOIs. Researchers can also become verified users and link their ORCID profiles to their Dockstore account, as described in this blog post.
Additionally, if you wish to cite the Cromwell execution engine or the WDL themselves, as is the case when you are publishing analyses using one of the Broad Institute's workflows, you can do so using the example below:
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)
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 are planning to write a manuscript about Terra, and once that is published or posted as a pre-print, we will update this article with full citation information.