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(how to) cite FireCloud, Cromwell, or WDL in your publications

Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Broadie, Moderator admin

WDL/Cromwell
See this WDL/Cromwell article for the citation.

FireCloud
If you are simply looking for a way to cite FireCloud you can cite this paper:

Birger C, Hanna M, Salinas E, Neff J, Saksena G, Livitz D, Rosebrock D, Stewart C, Leshchiner I, Baumann A, Voet D, Cibulskis K, Banks E, Philippakis A, Getz G. 2017. FireCloud, a cloud-based platform for collaborative genome analysis: Strategies for reducing and controlling costs bioRxiv doi: 10.1101/209494

Share your workspace or methods with reviewers:
To facilitate the examination of your data by reviewers, the workspace(s) and method(s) can be listed as separate entries as shown below. Share the method and workspace with the reviewer’s FireCloud accounts in order for them to access. Once you are ready to publicize the method to the community, set the permission to “publicly readable.” You can also think about featuring your workspace to make it easy for others to reproduce your analysis.

Structure:
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

Example Workspace:
Shifaw, B. (2018, January 9) help-gatk/Somatic-CNVs-GATK4 [workspace] Retrieved May 10, 2018 from https://portal.firecloud.org/#workspaces/help-gatk/Somatic-CNVs-GATK4

Example Method:
Shifaw, B. (2018, April 27) gatk/CNV_Somatic_Pair_Workflow (Snapshot ID 7, Submission ID e8981863-1482-4e12-a700-bd0ee9789692) [method] Retrieved May 10, 2018 from https://portal.firecloud.org/#workspaces/help-gatk/Somatic-CNVs-GATK4/monitor/e8981863-1482-4e12-a700-bd0ee9789692

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