Release notes

January 11th, 2021

ImprovementsTask queueing improvements

We have made the following changes to the task queueing process that should improve the queueing logic and contribute to faster completion of initialized tasks and analyses:

  • If you reach your parallel instance limit with running tasks, and there are both tasks and Data Cruncher analyses waiting in the queue, Data Cruncher analyses will be first to execute once instances become available.
  • If the parallel instance limit is reached with tasks that are being executed, when an instance becomes available it will first be allocated to running multi-instance or scattered tasks if they need additional instances. If there are no such tasks, the instance will be allocated to other task(s) that are next up in the queue. This will enable faster completion of multi-instance and scattered tasks and help avoid breaks in their execution.

Recently published apps

GENESIS LocusZoom visualizes association testing results using the LocusZoom standalone software. This app is a wrapper around LocusZoom standalone software to enable it to work with outputs of GENESIS association pipelines. The main goal of this app is to visualize results of GENESIS Single Variant Association Test, however regions from sliding window or aggregate tests with p-values below a certain threshold can be displayed in a separate track.

SBG Loci Snapshoter generates screenshots of specific regions across all aligned files provided as inputs. It utilizes the IGV batch functionality to create PNG images of desired loci across multiple samples. The main driver of developing this tool was doing a post-association visualisation of associated variants across a subset of CRAM files used to obtain those variants.

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December 24th, 2020

ImprovementsData Cruncher Stability and Usability Improvements

Your experience with Data Cruncher just got better thanks to the following improvements:

  • Use the full potential of RStudio as it is now officially out of the BETA stage and its stable release is available in Data Cruncher.
  • Maintain full control over your workspace integration capabilities in a more secure environment – your Data Cruncher sessions are now run on a separate domain providing even better security isolation and privacy control of your favorite third-party integrated development environments.
  • Have a better insight into your session initialization phase with a more informative loading experience.
  • Find your way around with more ease – the top navigation bar provides access to analysis information, control options, documentation and feedback form, while the editor continues to provide native experience in your chosen base environment.
    • Seven Bridges addons for JupyterLab (i.e. the Project Files tab and the Save to project right click option) are now deprecated in favor of a unified and improved experience – delivering a more stable and up-to-date visual interface you’re familiar with.
  • Enjoy the cost control capabilities (Suspend time) without getting interrupted – your keyboard and mouse activity in the editor is now monitored as session activity in all available environments.

Check out our documentation pages to find out more about Data Cruncher.

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November 30th, 2020

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.

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October 26th, 2020

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.

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October 19th, 2020

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.
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October 12th, 2020

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.

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October 5th, 2020

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.

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September 28th, 2020

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.

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September 23rd, 2020

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 RHEOVisual Interface can be found on GitHub

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We are always engaged in research and development, working to build the future of genomics, science, and health. Let's work together. We'd love to hear about your projects and challenges, so drop us a line.

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