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.
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. (2018, April 27) gatk/CNV_Somatic_Pair_Workflow (Snapshot ID 7, Submission ID e8981863-1482-4e12-a700-bd0ee9789692) [Workflow] Retrieved May 10, 2018 from https://portal.firecloud.org/#workspaces/help-gatk/Somatic-CNVs-GATK4/monitor/e8981863-1482-4e12-a700-bd0ee9789692
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 such that the workspace is publicly readable. You can also think about featuring your workspace to make it easy for others to reproduce your analysis.
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Full-stack genomics pipelining with GATK4 + WDL + Cromwell [version 1; not peer reviewed].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.