Release notes

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.

ReleaseSeven Bridges publishes the GRAF Germline Variant Detection Workflow

GRAF Germline Variant Detection Workflow has been published in the Public Apps Gallery, freely available for all Platform users. The GRAF Germline Variant Detection Workflow enables accurate alignment and variant calling by utilizing a genome graph that can overcome the limitations inherent in linear genome references. For use with this pipeline, two Pan-Genome graphs, compatible with GRCh37 and GRCh38 reference versions, are also published in the Public Reference Files. Detailed instructions on how to use the workflow are available in the workflow description. Results on the performance and accuracy of GRAF are discussed in this blog post by the GRAF team. If you do not currently have an account on the Seven Bridges Platform, read more about Seven Bridges GRAF on our website.

Supported instances update

With this update you can now use the newest instance sizes for Amazon EC2 C5, R5 and M5 Instances in task executions and Data Cruncher analyses.

The following instances have been added:

• c5.12xlarge (48 vCPU, 96 GiB memory, EBS-only)
• c5.24xlarge (96 vCPU, 192 GiB memory, EBS-only)
• r5.8xlarge (32 vCPU, 256 GiB memory, EBS-only)
• r5.16xlarge (64 vCPU, 512 GiB memory, EBS-only)
• m5.8xlarge (32 vCPU, 128 GiB memory, EBS-only)
• m5.16xlarge (64 vCPU, 256 GiB memory, EBS-only)

Learn more about supported instance types.

Recently published apps

Single-Cell Smart-seq2 Workflow v3.0.0

This workflow is designed by the Data Coordination Platform of the Human Cell Atlas to process single-cell RNAseq (scRNA-seq) data generated by Smart-seq2 assays. It enables processing of stranded or unstranded, paired-end or single-end, scRNA-seq data from individual cells.

Recently published apps

The RSEM toolkit and workflow were upgraded to CWL1.0 and updated to the latest versions.

Disabling of inactive user accounts

As a part of the ongoing effort on maximizing the security of the Seven Bridges Platform, we have started identifying inactive user accounts, which will be temporarily disabled in the upcoming period. This procedure is in line with recommendations and best practices for additional data security and prevention of unauthorized access to the system.

User accounts that will be labelled as inactive are those that haven’t logged in to the Platform or used the API in 90 days. Prior to temporarily disabling inactive accounts, notification emails will be sent out to their owners, inviting them to log in to the Platform if they want to keep their accounts active. Accounts that do get disabled will not be removed and data associated with them will remain on the Platform. They can be re-enabled at any time by emailing our Support Team at support@sbgenomics.com.

Finally, please note that this process will be continuous. This means that account inactivity will be constantly monitored and the procedure of sending notifications and disabling user accounts will be automatically carried out for any account that reaches the specified period of inactivity.

ImprovementsSimpler deploy of automation code packages

We have updated our Automation Development Kit (ADK) to simplify the process of creating and deploying code packages to the Seven Bridges Platform. 

The new ADK command for creating code package files that are executable on the Seven Bridges platform is called ‘freyja build‘ and is available in Freyja version 0.16.3 or higher. It checks the correctness of your project structure and content before it creates the code package, which helps avoid unnecessary execution failures. The new command also allows you to exclude certain files from the build process (for example config files containing your personal secret settings) and to specify project-external directories to be included in your code package (for example a shared Python library used across different automations). Please refer to the ‘freyja build‘ command synopsis for further details. The old command ‘freyja pack‘ has been deprecated.

Uploading code package files to the Seven Bridges Platform has also become much easier. Instead of first uploading the code package file to a Seven Bridges project that then needs to be linked to the automation, you can now upload code package files directly into the automation vault in a single step. Please refer to the Seven Bridges CLI command ‘sb automations packages create‘ for further details (version 0.12.3 or higher).

A step-by-step tutorial for the new deployment process is available online.

To make use of these new features, please pip-upgrade to the latest version of the ADK and install the newest version of the SB CLI.