Release notes

Recently published apps

The following apps have been ported to CWL 1.0 and are now available as CWL 1.0 apps in the Public Apps gallery:

• Optitype 1.2
• VEP annotation workflow 90.5
• Ensembl-VEP 90.5

Writing rate limit-efficient API scripts

The API rate limit is a limit to the number of calls you can send to the Seven Bridges API within a predefined time frame. That limit is 1,000 requests within 5 minutes. After this limit is reached, no further calls are accepted by the API server until the 5 minute interval ends.

It is important to write API scripts with this API rate limit in mind to minimize the number of API calls to the Seven Bridges Platform. This way, you avoid reaching your rate limit and your API scripts can execute without delay due to server-side throttling.

We put new documentation online that helps you make your API scripts rate limit-efficient. Code snippets demonstrate recommended use of the Seven Bridges Python client to minimize API calls for common tasks, including finding projects, iterating over result sets of queries, importing files from volumes, exporting files to volumes, updating file metadata, copying files between projects, deleting files, and submitting tasks for execution.

If you ever experienced errors or delays due to the Seven Bridges API rate limit, please make sure to give this new content a read to learn how to make your API calls (not) count.

NewSeven Bridges Automation Tools and Services

The new Seven Bridges Automation Tools and Services enable biotechnology and biopharmaceutical companies to increase productivity by bringing a diverse set of users into one environment. Scripts written with the Python Automation Development Kit (ADK) automatically gain concurrency, dependency management, memoization, retries, execution logs, and much more, enabling developers to focus on business logic and ultimately, reduce their lines of code by up to 80%. Within the same environment, end users are now able to process complex analysis workflows with the push of a button, share results instantly, and achieve total reproducibility.

Visit sevenbridges.com/automation for more details.

Supported instances update

You can now use next generation AWS Memory Optimized instances (R5) in task executions and Data Cruncher analyses. R5 instances support the high memory requirements of certain applications to increase performance and reduce latency.

Learn more about supported instance types.

NewNew CWL web editor is now live

We have released an updated version of our CWL web editor. This release integrates the functionality of our desktop editor, Rabix Composer, with the Seven Bridges Platform.

What’s new:

• Ability to edit both CWL sbg:draft-2 and v1.0 apps and select the CWL version before creating an app.
• Streamlined tool editor with all parameter sections available in a single continuous page. It’s now easier to have an overview of the way the tool was built.
• Optimized design of the workflow editor to facilitate working with large and complex workflows. When selecting a node, you’ll be able to see what its direct connections are.
• CWL Code editor in addition to the Visual Editor. For people who feel comfortable with writing raw JSON, we have enabled the code editor. All changes that you make in the code editor will be reflected in the visual editor and vice versa.
• Better documentation. We have expanded the documentation with our best practices for more advanced users.

If you have been using the Seven Bridges Platform for a while, don’t worry, the legacy editor will be available in case you don’t feel comfortable with making this transition right now. Note that the legacy editor can only be used to edit sbg:draft-2 CWL apps.

Multi-cloud

If you store your files on AWS US East (N. Virginia) and/or AWS US West (Oregon) regions, the Seven Bridges Platform now allows you to manage all your work from a single space and spin up chosen computation resources at the location where your data lives. By letting you choose your Project location, Seven Bridges provides an environment for much easier control of costs caused by potential data transfers between different regions. This way you can optimize your workload for a specific use case, and Seven Bridges will continue to provide full transparency over data transfer costs charged by cloud infrastructure providers. Read more.

Recently published apps

BROAD Best Practices RNA-Seq

This workflow represents the GATK Best Practices for SNP and INDEL calling on RNA-Seq data. Starting from an unmapped BAM file, it performs alignment to the reference genome, followed by marking duplicates, reassigning mapping qualities, base recalibration, variant calling and variant filtering. We used Broad’s best practice script in WDL format as a reference to create the BROAD Best Practices RNA-Seq Variant Calling 4.1.0.0 workflow in CWL version 1.0.

BROAD Best Practices Somatic CNV Panel Workflow

BROAD Best Practices Somatic CNV Panel Workflow is used for creating a panel of normals (PON) given a group of normal samples. Using read coverage collected over specified intervals, this workflow creates a panel of normals HDF5 file which is used in BROAD Best Practices Somatic CNV Pair Workflow for standardizing and denoising read counts. This workflow represents a CWL implementation of Broad’s best practice CNV panel WDL workflow.

BROAD Best Practices Somatic CNV Pair Workflow

BROAD Best Practices Somatic CNV Pair Workflow is used for detecting copy number variants (CNVs) as well as allelic segments. Given a tumor and optional matched normal sample, as well as panel of normals (PON) file, this workflow models and calls CNV segments. This workflow represents a CWL implementation of Broad’s best practice CNV pair WDL workflow.

NewMemoization (beta)

When defining task execution settings, you can now enable memoization. Achieve significant time and cost optimization of your project workload by letting the Platform reuse existing results of your previous runs. Memoization can be enabled at project or task level, where the task-level setting overrides the project-level one.

Learn more from our documentation.

NewMultiple datasets selection for querying in Data Browser

With multiple dataset selection for simultaneous querying, you are now able to start data querying in Data Browser by selecting more than one dataset. This allows you to search selected datasets by common entities (e.g. Case) and property values (e.g. male for the gender property), and get combined results from selected datasets. In addition, you can select only those instances for an entity (e.g. Case identifier) that are common in all selected datasets, if such instances are available. Those can then be filtered further by other entities/properties that the common instances have in selected datasets.

Additionally, the List (table) view on the Data Browser page has been removed and priority has been given to the Detail page.

ImprovementsImproved organization of Public Reference Files

The Public Reference Files gallery has been renamed into Public Files and split into two categories, Public Reference Files and Public Test Files, where the former holds all common reference files, while the latter contains common test samples. Both of these categories can be accessed from the Data menu on the main menu bar.

This change does not affect the API, so all related API calls remain the same.

NewAdded support for GPU Instances

The first family of GPU instances we’re introducing is Amazon EC2 P2. P2 Instances are powerful, scalable instances that provide GPU-based parallel compute capabilities. Designed for general-purpose GPU compute applications using CUDA and OpenCL, these instances are ideally suited for machine learning, molecular modeling, genomics, rendering, and other workloads requiring massive parallel floating point processing power. NVIDIA drivers come preinstalled and optimized according to the Amazon best practice for the specific instance family and are accessible from the Docker container.

The following instances have been added:

• p2.xlarge
• p2.8xlarge
• p2.16xlarge

Learn more about GPU instances on the Platform.

Spot Instances enabled by default on project creation

In order to promote execution cost optimization, Spot Instances are now enabled by default when creating a new project through the visual interface or the API, unless you have specifically set otherwise. This setting can later be changed from the project settings page, or overridden per task on the draft task page. Learn more about Spot Instances on the Platform.

NewSupport for asynchronous bulk actions through the API

As a part of adding full support for folders and improving scalability, we have introduced asynchronous file system actions through the API. Currently supported actions are copy and delete, and these are enabled for both files and folders. There are five new API endpoints for async bulk actions which can be used for issuing copy and delete commands and for getting job statuses. This enables the following API actions which weren’t possible before:

• Copy folder (along with the files it contains and the underlying folder structure)
• Bulk copy of files and folders into different paths (project root or specific folder inside the project)
• Delete non-empty folder

Learn more from our documentation.

ImprovementsImproved layout of the draft task page

In order to streamline the preparation process for task execution, both file inputs and app settings will now be available as two columns under the same tab named Task Inputs on the draft task page. Spot Instance configuration will be moved to the second tab on the draft task page, named Execution Settings. This tab will also serve as the central and unique location for all settings related to task execution that will be added in the future.

ImprovementsSecurity enhancements

In order to enhance our comprehensive security framework and provide our enterprise customers with additional options for securing their data and analyses on the Seven Bridges Platform, we are introducing the following security enhancements:

• Multi-factor authentication
• Shorter idle session logout time

Multi-factor authentication

Multi-factor authentication (MFA) significantly decreases the risk of compromising user accounts. It is an additional layer of protection beyond your password and combines something you already know (password) with something you have (mobile phone). You will have the option to use your email or an authentication app as the second step in the authentication procedure, or use backup codes if the preferred authentication method is not available. We also offer the popular “remember me on this computer” option that increases the usability of this security feature, as you will not be asked for the second factor on a specific computer during a specific time period. Moreover, in case of problems with the login procedure, there will be an option to contact support directly from the login screen. Learn more about MFA from User documentation and Administrator documentation.

We also enable the enterprise administrator to:

• Define whether multi-factor is forced on all users in an enterprise
• Define whether the “remember me on this computer” option is available, as well as the number of days after which the user will be asked for the second factor again.

Shorter idle session logout time

We have reduced default idle session logout time to 1 hour on the Seven Bridges Platform (both USA and EU installations), thus enabling our enterprise customers to be compliant with the required security standards. This means that users who have been inactive for the defined period of time will be logged out. This will affect all Platform users.

Single sign-on

We would also like to remind you of our Single sign-on solution, which enables our enterprise users to integrate their own SAML-based single sign-on solution with the Platform. If you are an enterprise user, this way you can improve your security by minimizing the number of logins you need to manage for your users and re-use already existing security infrastructure, together with improving user experience. If you wish to set this up, feel free to contact our support.

Recently published apps

Metagenomics WGS Functional Profiling – HUMAnN2

HUMAnN2 (the HMP Unified Metabolic Analysis Network) is a tool used for efficiently and accurately determining the presence/absence and abundance of metabolic pathways in a microbial community from metagenomic sequencing data. It introduces a novel tiered search algorithm that provides highly accurate profiles for characterized members of microbial communities, with fallback to translated search for uncharacterized members.

Metagenomic WGS Functional Profiling – HUMAnN2 workflow provides a complete functional profiling analysis of input samples, designed to analyze several metagenomics samples in parallel.