Release notes

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.

Recently published apps

Salmon, DeepVariant and STAR-Fusion were updated to the latest versions.

Data model updates

Data models have been changed for a series of datasets on the Seven Bridges Platform. You will be notified about the change through an info message next to your saved Data Browser queries, informing you that the queries might be affected by the data model update and instructing you to rebuild the queries that are not working, or contact Seven Bridges for assistance.

ImprovementsData Cruncher file preview improvements

We have improved the file preview option in Data Cruncher analysis details to support additional file formats. The full list of supported formats now includes IPYNB, HTML, PDF, JPG, JPEG, SVG, PNG, GIF, MD, and raw content preview is available for all other text file formats, for example RMD, R, PY, etc.

Recently published apps

Cutadapt was updated to the latest version and upgraded to CWL1.0.

NewData model versions

To help you maintain your dataset queries and align them with changes in underlying data models, we have introduced data model versioning.

Data models determine the nomenclature for all elements that are included in a model, define all entities and their properties, as well as relationships between different entities. When there is a new version of a data model, the structure of these elements and their relationships can change, thus rendering previously saved queries non-runnable.

To make the changes more visible and help you rebuild your queries, data model versions are displayed at various locations in the Data Browser for each of the available datasets, as well as the update history. Learn more

Recently published apps

DESeq2 was updated to the latest version and upgraded to CWL1.0.