Frequently Asked Questions

The CGC Knowledge Center holds extensive documentation for how the platform works and how to access data. It is always the best source of information.

However, we’ve collected short answers for our most common questions here.

Email us if there’s something else that you need!

  • We generally recommend first creating a project. You can do this by selecting “Projects” on the top blue banner, then click on “Create a Project”. From this new project space, you’ll be able to select and access data, add or create tools, and finally run an analysis.

    For more information, please watch our “Getting Started On The CGC Platform” video tutorial.

  • Each new user to the CGC will be provided with $300 of pilot funding, courtesy of the NCI. Feel free to use these funds to get acquainted with the platform and run a few analyses.

    Invoiced billing groups (either billed monthly or through PO) can be requested from Seven Bridges staff.

    For more information, please watch our “Billing Groups and Pilot Funding” video tutorial.

  • Once you’ve created a project, you can easily add members as collaborators. To do this, select the “invite new members” button on the right hand side of your main project dashboard. You can search for members by username or by typing their email address. Once you’ve invited a collaborator, you can set permissions and choose whether you’d like for them to be able to write, copy, execute or serve as an admin to your project.

    For more information, please watch our “Projects Creation and Collaboration” video tutorial.

  • Using your own scripts on our platform is very simple. You can choose to:

    1) Analyze data directly using an Interactive Analysis instance (Currently, we have RStudio and Jupyter Labs available); or

    2) Create an app using CWL that utilizes your scripts to analyze data with the click of a button

    For help with anything, reach out to us or visit our Office Hours Tuesdays @ 10 am ET & Thursdays @ 2 pm ET

  • Workflows on the CGC are specified using the Common Workflow Language (CWL) through a drag-and-drop workflow editor. The Cancer Genomics Cloud natively supports CWL. Existing CWL workflows (in YAML code) can also be ported to the CGC with minimal editing.

    Nextflow is a command line scripting tool that allows users to add or modify parameters for many different tools without needing the exact syntax.

    CWL has these same parameters available to users, usually cleaned up and hidden within the app. CWL can be as simple or as complex as the user wants and tools or apps can be easily manipulated with toggling options or adding parameters within the tool/app.

    As of now, we have limited support for Nextflow, but contact us if you wish to use Nextflow.

  • Troubleshooting failed tasks is one of the primary things we do in Office Hours but if you can’t make it, we do have a guide to how to figure out what went wrong with your task.

    See: Troubleshooting tutorial which is paired with the “Troubleshooting Failed Tasks Public Project”.