Release notes

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.

Memoization (WorkReuse) – Stable Release

With this release, Memoization (WorkReuse) is now officially stable and is no longer in the BETA stage.

Furthermore, for CWL 1.1 apps, you can now also disable the reuse mechanism on the tool level, using the CWL v1.1 WorkReuse feature. For specifics on which tools this mechanism should be disabled, please refer to our Memoization documentation.

ImprovementsSeven Bridges Command Line Interface Improvements

This release improves the Seven Bridges Command Line Interface (SB CLI) by adding the new troubleshoot command that provides a convenient way for you to include all relevant log information when reporting a problem with the SB CLI. The command generates a local debug file which, once generated, should be sent to the Seven Bridges Support Team. The file will contain relevant information that should help Seven Bridges engineers identify the problem. Also, the SB CLI executable is now signed with the Seven Bridges certificate.

NewNew Data Cruncher Environment Setups Available

The list of available Data Cruncher environment setups has been updated to support more recent Python and R versions. Precisely, JupyterLab now has a new SB Data Science environment setup that supports Python 3.8 and R 3.6, while RStudio has a new SB Bioinformatics setup that supports R version 4.0. See our documentation for details about available libraries and their versions.

ReleaseReal-time Job Monitoring and Instance Metrics – Stable Release

With this release, Real-time job monitoring and Instance metrics are now officially stable and are no longer in the BETA stage. This release includes several minor bug fixes and improvements that contribute to the overall stability and robustness of the feature. Learn more about real-time job monitoring and instance metrics.

NewConnecting AWS volumes using IAM roles through the visual interface

Connection of Amazon Web Services S3 buckets with the Seven Bridges Platform using IAM roles is now also available through the connection wizard in the visual interface. The new connection option that uses IAM roles provides improved security for connecting cloud storage to the Platform and greater flexibility by allowing you to choose between the IAM user or IAM role connection method. For both IAM role and IAM user, as an AWS identity, you can set permission policies to define what another identity associated with them can and cannot do on your bucket. In addition to that, an IAM role provides temporary security credentials which the Platform automatically renews when the user’s bucket is accessed through the Platform, thus increasing the security of the established connection. Learn more.