Release notes

NewData Cruncher – RStudio (beta)

In addition to JupyterLab, Data Cruncher now supports one more development environment, RStudio. You can choose between the two environments when setting up your Data Cruncher analysis.

Also, file saving rules have been deprecated, so all analysis files will be automatically saved in your analysis workspace on the Platform, regardless of their size or extension.

Learn more about RStudio in Data Cruncher from our documentation.

NewHuman Cell Atlas Preview Datasets public project

Human Cell Atlas Preview Datasets are now available as a public project on the Seven Bridges Platform. The project contains files released to the research community within the first three single-cell sequencing datasets as “Human Cell Atlas Preview Datasets”. The available datasets are:

• Census of Immune Cells
• Ischaemic Sensitivity of Human Tissue
• Melanoma Infiltration of Stromal and Immune Cells

The Human Cell Atlas

Launched in 2016, the Human Cell Atlas (HCA) is an international collaborative effort to catalog all the cells in the human body in terms of their distinctive patterns of gene expression, physiological states, developmental trajectories, and location to understand how genetic variants impact disease risk, define drug toxicities, discover better therapies, and advance regenerative medicine. Learn more.

Read the documentation and see the Human Cell Atlas Preview Datasets public project on the Seven Bridges Platform.

ImprovementsFolders as task inputs and outputs

When selecting inputs for a task, you will now be able to select an entire folder for input ports that are set up to take folders as input values. This means that such input ports will take all files from the root of the selected folder and its subfolders. Folders can now also be displayed as app outputs, provided that the app itself is configured to produce output data in folder(s). This feature is available for CWL 1.0 apps only.

ImprovementsComputation backend improvements

We are making some improvements to our computation backend. These changes impact sbg:draft2 tasks only, mostly bringing some of their behaviors/capabilities in line with CWL 1.0 tasks.

The following are the changes:

Scattering improvement: When running sbg:draft2 workflows, you might notice a runtime improvement in some workflows that make use of chained scattering. There is no action needed on your part and you can continue running your apps as usual.

Docker entrypoints: The executor for sbg:draft2 apps now honors docker image entrypoints. If your sbg:draft-2 app refers to a Docker image that has a defined entrypoint, this previously ignored Docker feature will now be active. Please have this change in mind when running the app and do let us know if you notice any unexpected behavior.

Stage multiple files with the same name: If multiple files that have the same name are provided from an upstream tool to a staged input port of a downstream tool in a workflow, staging will work successfully as the files will now be renamed automatically. Please have this in mind if you are relying on file names during the processing steps in your workflows.

If you have any questions related to these changes, please contact our Support team at support@sbgenomics.com.

Recently published apps

DeepVariant 0.7.2 is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is highly accurate, robust, flexible and easy to use. To use DeepVariant on the Seven Bridges Platform, simply supply it with reads, reference, and select the desired model to use (WGS or WES).

Deprecation of Previous Generation instance types

To further optimize user workloads, we have decided to deprecate some of the oldest Previous Generation AWS instances.

The following AWS instance types are no longer supported through the Seven Bridges Platform:

• m1.small
• m1.medium
• m1.large
• m1.xlarge
• m2.xlarge
• m2.2xlarge
• m2.4xlarge
• c1.medium
• c1.xlarge
• cc2.8xlarge
• cr1.8xlarge

Please see the full list of supported instance types and the official recommendation for Upgrade Paths from AWS.

If you have an app with one of these types set as instance type hint, it will automatically be migrated to use the most appropriate newer instance type.

ImprovementsQuery projects by name in the Python API client

If you are using the sevenbridges-python API client, you are now also able to query projects by project name. When querying with the name parameter, partial matching is performed and the result is returned as a list. See an example in the List Projects section of sevenbridges-python documentation.

ImprovementsFolder options for FTP/HTTP(S) import

When importing data from an FTP or HTTP(S) server to the Platform, you are now able to import an entire folder structure in the exact same form as it appears on its source server, or choose to “flatten” the structure and import the files only. Also, the Platform now provides a selection of naming conflict resolution options for FTP/HTTP(S) imports. If an item that is being imported has the same name as an item already present at the target location, you can select whether to skip importing the item, overwrite the existing one or auto-rename the one that is being imported. Learn more.

ImprovementsR client updates

The sevenbridges-r API client has been updated with several sets of API calls. Precisely, the new additions include Folders, Enterprise, Bulk, Actions and Markers (Advance Access) APIs. Moreover, the R client now also supports setting execution hints per task run when drafting new tasks.

In order to improve your experience with our R client, we have optimized package installation and loading time. Also, the documentation website for the R client has been updated with new styling and improved text readability. To download the latest version and get more information, please visit the Releases page on GitHub and read the documentation.

NewNew file search option

When searching for files within a project, now you have the option to search within the current folder only, without including subfolders and their content in the search. Until now, the default behavior was that the current folder (or project root) and all of its subfolders got included in the search, with the Path column being shown in the search results. This remains the default behavior, but now there is an additional option to search through items from the current path (project root or folder) only, without searching through subfolders.

One of the two file search options can be selected by clicking the search icon within the file search field. Learn more.

ImprovementsOpen apps for editing in web editors more easily

The option to edit apps in the tool or workflow editor on the Platform is now more accessible through the visual interface. When the Edit option is clicked for an app, all sbg:draft-2 apps will be opened in the corresponding web editor by default. However, you still have the option to edit sbg:draft-2 apps in Rabix Composer, our standalone app editor from the Rabix toolkit. For now, Rabix Composer also remains the only editor for CWL 1.0 apps.

Recently published apps

Control-FREEC 11.5

Control-FREEC analyzes copy-number alterations in exome and whole-genome DNA sequencing. This tool computes, normalizes and segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.