Release notes

ImprovementsImproved project member permissions for Enterprise users

We have introduced minor changes to the project permission system for Enterprise clients on the Seven Bridges Platform. These changes provide enhanced security features and increased usability for our users. 

Enterprise Division members now have more options when creating projects on the Platform. When creating a project, Division members will now automatically inherit Admin project permissions. Please note, this change only applies to projects that will be created in the future. 

Furthermore, project creators will be able to modify project names, lock projects, and modify project execution settings (for example spot instance usage, memoization, duration of intermediate files retention), regardless of their Enterprise role (Division Admin or Division Member). 

Additionally, the ability to manage project members now requires the Project Admin permission, meaning only Project and Division Admins will be allowed to manage project members. Project members without Admin permissions are no longer able to add members to projects.

Finally, only Division Admins can delete projects, which provides additional security against intentional or unintentional project deletion.

The same permission changes also apply to Docker repositories and volumes.

Recently published apps

Strelka2 Somatic workflow and Strelka2 Germline tool have been published to the Seven Bridges Platform in CWL1.0. Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. For better calling results structural variant caller, Manta has been added to the Somatic Workflow.

NewUpload files directly through the visual interface

Uploads just became way easier! In order to enable easy and convenient small-scale file uploads for our users, we have added a new functionality that allows you to upload files directly through the Platform’s visual interface. To upload files from your local storage, navigate to the desired project and click the Add files button. You will notice a new tab called Your Computer, which will, apart from file upload itself, provide all standard upload-related features such as naming conflicts resolution, file tagging and tracking of upload progress. Learn more.

Recently published apps

The updated GENESIS apps are now available in our public apps gallery. The new release includes:

• New Docker image v.2.8.1.
• Updated input and output descriptions.
• Comprehensive benchmarking included in the apps description.
• Standard output included in the task logs.
• Other minor changes.

Recently published apps

The EPACTS 3.4.2 toolkit has been published in CWL1.0. EPACTS (Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers.

Recently published apps

Plink1.90 and Plink2.0 have been published in CWL1.0. Plink is a widely used open-source tool for genome-wide association studies and research in population genetics. It can rapidly manipulate and analyze large datasets in their entirety; data management, summary statistics, population stratification and association analysis are only some of Plink’s domains of function.

Division administrators can disable division users via the API

A new functionality has been added to the Enterprise API to allow division administrators to disable division users (remove users from the division) via the API.

Recently published apps

MultiQC has been upgraded to CWL1.0, updated to the latest version, and published on all environments.

NewThe Seven Bridges Platform now offers a graphical user interface for automated workflows

Seven Bridges RHEO™, our new product line for platform automations, now offers a visual interface (GUI). The new visual interface allows automation users to start and monitor their automation runs via the Seven Bridges visual interface, which complements the already existing command line interface (CLI) that was released last year. 

The visual interface renders individual automation inputs and outputs as clickable platform entities based on type information provided by the automation developer inside the automation code. Older automation code packages without type information are supported as well and their inputs and outputs are rendered as generic multi-line text boxes in JSON format.

More extensive user and developer documentation is available in our Knowledge Center.

Example code that shows how to make use of the new RHEO™ Visual Interface can be found on GitHub. 

NewCWL 1.1 Now Available on the Seven Bridges Platform

Seven Bridges Platform now supports Common Workflow Language (CWL) v1.1. The new version of CWL brings some minor improvements, most notably:

• Limit for execution time of a command line tool. If execution time exceeds the defined limit, the tool will fail in order to prevent additional costs.
• Option to disable memoization for a specific tool. If you want to use memoization for a workflow run, but want to skip memoization in a specific tool, CWL1.1 introduces a feature that allows this.
• Ability to declare optional secondary files. A task is not prevented from running if an optional secondary file is not available in the project.
• And quite a few minor features and improvements. For the detailed change log please see the CWL CommandLineTool specification and the CWL Workflow specification.

The new CWL version v1.1 is a backwards-compatible upgrade of version v1.0, meaning all v1.0 features are still supported in v1.1. To upgrade a v1.0 app to v1.1, simply edit the app and the next version of the app can automatically be upgraded to v1.1. (Note that upgrading a workflow CWL version to v1.1 this way will not upgrade the CWL version of tools in the workflow).

CWL v1.0 apps are still supported and can be used in workflows in combination with CWL v1.1 apps.

Deprecation of Previous Generation Instance Types

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

We are removing support for the following AWS instance types from the Seven Bridges Platform:

• c3.large
• c3.xlarge
• c3.2xlarge
• c3.4xlarge
• c3.8xlarge
• m3.medium
• m3.large
• m3.xlarge
• m3.2xlarge
• r3.large
• r3.xlarge
• r3.2xlarge
• r3.4xlarge
• r3.8xlarge

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

If you are explicitly setting some of these types via the API, please update your scripts before September 15th.

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