Release notes

Rabix Composer v1.0 Release

We’ve released the initial version of Rabix Composer (v1.0), which includes significant improvements over the beta version with respect to the development of CWL 1.0 and sbg:draft-2 applications on your local machine.

Set suggested files for workflow inputs

We’ve introduced the option to set files from public projects as suggested for a file input in a workflow. This will allow anyone who runs the workflow to use the suggested files as inputs in a single click, and only have to add the remaining input files manually. Please refer to documentation for more details.

Release notes

Folders on the visual interface

We have introduced support for folders on the CGC. To complement our existing API functionalities, now you can organize your project files into folders through the CGC's visual interface, which allows you to have a better overview of your files and manage them more easily.

Smart Variant Filtering

The variant filtering process consists of selecting highly confident variants and removing the ones that are falsely called. This process used to be mostly left out from deeper testing in secondary genomic DNA analyses, even though it can boost precision of variant calls significantly. After developing graph genome alignment tool and reassembly variant caller, we are now launching the Smart Variant Filtering tool used for filtering germline variants.

Release notes

TLS 1.0 and TLS 1.1 no longer supported

We have removed support for TLS 1.0 and TLS 1.1 protocols. The only supported protocol on the CGC and the CGC API is TLS 1.2. If you are using a client that does not support TLS 1.2, please perform an upgrade to continue using the Cancer Genomics Cloud.

Release notes

EXPORT TO VOLUMES: COPY-ONLY PARAMETER

We've added an Advance Access copy-only parameter to the Start an Export job request for Volumes. This means that, while it is fully operational, it is subject to change. If this parameter, copy_only, is set to true, the specified file will be copied to a volume but the source file will remain on the CGC. Learn more from our documentation.

Release notes

SUPPORT FOR AMAZON WEB SERVICES SPOT INSTANCES

Seven Bridges has introduced support for Spot instances on the Amazon Web Services (AWS) deploy of the Cancer Genomics Cloud. Spot instance support can be selected as a default for projects and and an option for each task execution. By selecting a spot instance execution costs can be dramatically reduced. Our testing indicates an execution cost savings of over 75% on common workflows.

Release notes

DATASET IMPROVEMENTS

TARGET GRCh38 Dataset

The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) dataset provides genomic, transcriptomic, and epigenomic data from patients representing several childhood cancers and serves as a valuable complement to the existing genomic and multi-omic datasets available on the CGC. The complete TARGET GRCh38 dataset, which includes both Open Data accessible to all researchers and Controlled Data, to which access is regulated by the Database for Genotypes and Phenotypes (dbGaP), is now available on the CGC. This dataset can be queried using the Data Browser to generate custom cohorts from within this dataset as well as cohorts derived from multiple similarly aligned datasets such as the TARGET GRCh38 and TCGA GRCh38 datasets.

Release notes

ELASTIC BLOCK STORAGE CUSTOMIZATION FEATURE

Overview

On August 1, we released a feature that provides you with the ability to customize the amount of Elastic Block Storage (EBS) disk space attached to different Amazon instance configurations. EBS customization is useful for bioinformatics workflows because it provides the ability to optimize your computation by giving you greater control over requirements and costs.

To learn more about EBS customization, please see our documentation.

Release notes

PARALLEL INSTANCE LIMITS AND TASK QUEUING

Individual users on the CGC now have a default usage limit of 80 parallel instances. Seven Bridges sets this upper bound because the number of parallel instances used in total by the CGC Platform is limited by Amazon Web Services (AWS), the CGC’s underlying cloud service provider. While this means that tasks using more than 80 instances can take longer to complete, it also helps ensure that instances are available for all CGC users to run their analyses.

Release notes

HARMONIZED DATASET ON THE CGC

Datasets on the CGC are now categorized as "harmonized" and "legacy" in accordance with the GDC.

In 2016, the GDC started hosting and distributing previously generated data from The Cancer Genome Atlas (TCGA). Additionally, for all submitted sequence data (FASTQs and BAM alignment files), the GDC generated new alignments (BAM files) to the latest human reference genome, GRCh38, using standard workflows. Using these alignments, the GDC generated derived data, including normal and tumor variant and mutation calls, gene and miRNA expression, and splice junction quantification data. The GDC refers to this process of data generation through standard workflows as data harmonization.

Release notes

EXPORT TO VOLUMES: COPY-ONLY PARAMETER

We've added an Advance Access copy-only parameter to the Start an Export job request for Volumes. This means that, while it is fully operational, it is subject to change. If this parameter, copy_only, is set to true, the specified file will be copied to a volume but the source file will remain on the CGC. Learn more from our documentation.

Release notes

SEARCH VIA THE DATASETS API

Use the Datasets API to search across datasets hosted on the CGC, such as TCGA and CCLE. First, use a free-text search to find all exact matches in metadata across all databases. Then, use the URIs obtained in the initial search to obtain further details, including individual members matching the designated resource. All responses are provided in the JSON format.

Learn more about searching via the Datasets API.