Recently published apps
The following apps had their versions updated and were bumped to CWL1.0:
- STAR Workflow
- Deep Variant
ImprovementsDocker 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.
Additionally, we changed the default privacy setting for Docker repositories to private. This change will only affect newly created repositories (when images are pushed for the first time to a non-existing repository). Privacy settings for existing Docker repositories remain the same as before.
For non-division users:
This release also introduces more strict repository naming. Users were previously allowed to push images under their username, but also to replace the “.” character with the “_” character and vice versa. Starting with this release, naming of the docker repositories must be concordant with usernames. Existing Docker images will, of course, be preserved in order to keep the functionality of existing workflows. For example: My username is
rosalind.franklin and I want to push an ubuntu image. I will name my docker repository
ReleaseGDC 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.
Bulk moving of files and folders via the API
In order to help you further optimize your API usage and the number of calls required to organize files and folders within projects, we have introduced the option of moving files or folders in bulk from one project location to another. Bulk move is aimed at improving API usage and user experience in general for all users who use the API to run analyses at scale. For more information, please see the related documentation pages:
Recently published apps
The following toolkits had their versions updated and were bumped to CWL1.0:
ImprovementsPassword policy changes on the Platform
In order to further increase the security of the Seven Bridges Platform and user data, we have enforced a stricter password policy. Specifically, the changes include:
- After 5 unsuccessful login attempts, you will be locked out of your account.
- When changing your password, you will not be able to set a previous password if it was already used in the past 365 days.
NewPlatform status page now available at status.sevenbridges.com
In order to enable easier communication of real-time Platform status, we have introduced the Platform status page at status.sevenbridges.com. The page covers the current state of several functional parts of the Platform, as well as our public website and the Platform’s documentation website. There is also an overview of past incidents and a detailed view of the complete incident history.
ImprovementsSearch by ID through multiple datasets at once
We have improved the existing Search by ID feature by enabling you to perform a search that will be applied across all available datasets. The search is performed by clicking Search by ID from the Data Browser’s dataset selection screen, returns sets of matched entities from all available datasets and allows you to select an entity (or a combination of entities) to start the Data Browser with. The search covers every available UUID and ID, either belonging to an entity or property, while retaining the existing capability of searching by file name.
NewRecently published apps
Several new CWL1.0 apps have been published to the Public Apps Gallery:
New BROAD Best Practices workflows: Data Pre-processing and Germline snps and indels variant calling in version 184.108.40.206. These workflows are built according to BROAD’s best practices following their WDL scripts, and together they allow for producing analysis-ready BAM files and VCF files with germline mutations.
eQTL analysis workflows: FastQTL and MatrixEQTL – Expression quantitative trait loci (eQTLs) are genomic variants related to variation in expression levels of mRNAs. These loci could be either cis, in the neighborhood of a gene transcription start site (TSS) or trans, distant eQTLs. The eQTL analysis workflow with FastQTL and MatrixEQTL are designed for fast eQTL analysis on large datasets, using standard mapping methods that test the linkage between variation in expression and genetic polymorphisms. FastQTL works with cis loci, while MatrixEQTL works with both cis and trans loci. These workflows are available on the Platform, starting from standard bioinformatics file formats (VCFs and gene expression results), and producing a comprehensive set of plots, reports and results allowing for easier insight into eQTL analysis.
NanoStringQCPro 1.10.0: NanoString® has introduced the nCounter technology for direct counting of molecules in samples, which enables direct detection of specific RNA, DNA and protein molecules. It provides highly robust data across clinically relevant samples while reducing hands-on time and simplifying analysis. The NanoStringQCPro app performs basic QC steps and data normalization of NanoString mRNA gene expression data.
NewAdded support for Amazon EC2 P3 GPU Instances
We have added support for Amazon P3 GPU instance family to the Seven Bridges Platform. Amazon EC2 P3 instances deliver high performance compute in the cloud with up to 8 NVIDIA® V100 Tensor Core GPUs and up to 100 Gbps of networking throughput. These instances deliver up to one petaflop of mixed-precision performance per instance to significantly accelerate machine learning and high performance computing applications.
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:
NewDefine Compute Resources per Task Run
When creating a task via visual interface, you are now able to set top level instance type and max number of parallel instances for your execution without having to create a new version of the app. Learn more about setting execution hints on task level from our documentation.