Release notes

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.

NewReal-time job monitoring / Instance metrics [BETA]

With these new features we are providing additional job monitoring and debugging tools, which are readily accessible for each task during its execution. You are now able to monitor execution progress in a more extensive way and find out the reasons for stuck, prolonged, or misconfigured jobs on your own, while we continue to ensure the same level of reproducibility.

Real-time job monitoring

As long as the instance on which the job was running is active, you can now access the following information about the job execution environment:

• Standard output and error streams.
• Workspace directory content and structure.
• Head/Tail preview of text file formats for files in the workspace directory.
• Instance metrics for the duration of the job.

Read more

Instance metrics

The Platform now also lets you access instance metrics information for all instances used in task execution. This information is available during task execution and for 15 days after the task has been executed. Read more

NewData Cruncher multiple environment setups

When selecting your Data Cruncher environment, you are now able to chose between different environment setups for your JupyterLab or RStudio analysis. Each environment setup is a set of preinstalled libraries that is available every time an analysis is started and is intended for a specific purpose.

For this first release, we are enabling support for machine learning use cases using CPU or GPU instances. Learn more.

ImprovementsTask validation allows additional characters in file names

We updated task validation to allow ~ (tilde) and # (hash) characters in input file names. When executing tasks on the Platform, you will be able to use input files containing those characters in their names.

Recently published apps

The following additions were made to the Public Apps Gallery:

• FastQC was updated to CWL1.0 and had it’s version bumped as well to the latest one.
• The seq2HLA tool was published in CWL1.0 as well. This tool does HLA typing from RNA-Seq data.
• Sleuth 0.30.0 was published in CWL1.0. This tool does differential expression analysis with results coming in from any of our favorite pseudoaligners (i.e. Salmon or Kallisto). The tool is wrapped in accordance with our existing differential expression tools (like DESeq2), so the user experience should be similar.
• Kallisto/Salmon Sleuth workflow was published, as a CWL1.0 app as well. This workflow is meant to provide end-to-end read quantification + differential expression solution, starting from FASTQ files and generating a differential expression report with Sleuth. The FASTQs are processed beforehand with either Kallisto or Salmon (as chosen), allowing for ultra-fast transcript quantification, so that Sleuth analysis can proceed in the fastest time possible.

Recently published apps

The following apps had their versions updated and were bumped to CWL1.0:

• STAR
• STAR Workflow
• STAR-Fusion
• Deep Variant