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.

Seven 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.

New 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.

Real-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.

Connecting AWS volumes using IAM roles through the visual interface

Connection of Amazon Web Services S3 buckets with the CGC 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 CGC and greater flexibility by allowing you to choose between the IAM user or IAM role connection method.

Troubleshooting guide now available for the CGC

To help you troubleshoot and debug failed tasks more easily, we have published a set of examples that show some of the common reasons for task failure, but also provide insight into more advanced debugging methods and tools. The guide consists of the Troubleshooting tutorial for the CGC, accompanied by the Troubleshooting Failed Tasks public project that is available in the Public projects section on the CGC. The public project contains all tasks described in the tutorial, and can be used to see how the troubleshooting examples work in practice.

Seven 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 CGC 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 CGC, read more about Seven Bridges GRAF on the Seven Bridges 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 on the CGC, 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 CGC or used the API in 90 days. Prior to temporarily disabling inactive accounts, notification emails will be sent out to account owners, inviting them to log in to the CGC 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 CGC. They can be re-enabled at any time by emailing our Support Team at support@sbgenomics.com.

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 CGC. 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.

Data 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.

Data 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.

Real-time job monitoring / Instance metrics [new feature, 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 additional information about the job execution environment.

Instance metrics

The CGC 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.

Data 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.

Task 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 CGC, 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.

PDC data update on the CGC

PDC data on the CGC has been updated to match the PDC Data Release from December 20, 2019.

New studies released:

• CPTAC GBM Discovery Study - Proteome

• CPTAC GBM Discovery Study - Phosphoproteome

• CPTAC GBM Discovery Study - CompRef Proteome

• CPTAC GBM Discovery Study - CompRef Phosphoproteome

The update includes 2090 files and ~500 GB of data.

See more information about the history and contents of each PDC data update on the CGC.

Recently published apps

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

• STAR

• STAR Workflow

• STAR-Fusion

• Deep Variant

Docker repository management improvements

With this release of Docker Repository Management improvements, we provide our users with a better user interface, as well as additional functionalities. The new Docker registry section under the Developer tab is introduced to:

• Provide more details on Docker images, such as tag, size, image ID, SHA digest, time of last update.

• Provide logs for all push and delete actions over a repository.

• Provide example command lines for docker login, push and pull commands.

• Allow users to delete a Docker repository or delete an image by tag.

• Allow users to manage Docker repository membership and permission level.

• Allow users to create new empty repositories. This means that users can now create a Docker repository and mark it as private before pushing any content (images) to the repository.

GDC Datasets version update

As of December 27, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 21.

Recently published apps

Tabix 1.9 toolkit was updated to CWL1.0.