NewCWL 1.1 Now Available on the Seven Bridges Platform
Seven Bridges Platform now supports Common Workflow Language (CWL) v1.1. The new version of CWL brings some minor improvements, most notably:
- Limit for execution time of a command line tool. If execution time exceeds the defined limit, the tool will fail in order to prevent additional costs.
- Option to disable memoization for a specific tool. If you want to use memoization for a workflow run, but want to skip memoization in a specific tool, CWL1.1 introduces a feature that allows this.
- Ability to declare optional secondary files. A task is not prevented from running if an optional secondary file is not available in the project.
- And quite a few minor features and improvements. For the detailed change log please see the CWL CommandLineTool specification and the CWL Workflow specification.
The new CWL version v1.1 is a backwards-compatible upgrade of version v1.0, meaning all v1.0 features are still supported in v1.1. To upgrade a v1.0 app to v1.1, simply edit the app and the next version of the app can automatically be upgraded to v1.1. (Note that upgrading a workflow CWL version to v1.1 this way will not upgrade the CWL version of tools in the workflow).
CWL v1.0 apps are still supported and can be used in workflows in combination with CWL v1.1 apps.
Deprecation of Previous Generation Instance Types
To further optimize user workloads, we have decided to deprecate some of the older Previous Generation AWS instances.
We are removing support for the following AWS instance types from the Seven Bridges Platform:
If you have an app, task or Data Cruncher analysis with one of these types set as instance type hint, it will automatically be migrated to use the most appropriate newer instance type.
If you are explicitly setting some of these types via the API, please update your scripts before September 15th.
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.
ImprovementsSeven 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.
NewNew 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.
ReleaseReal-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.
NewConnecting AWS volumes using IAM roles through the visual interface
Connection of Amazon Web Services S3 buckets with the Seven Bridges Platform 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 Platform and greater flexibility by allowing you to choose between the IAM user or IAM role connection method. For both IAM role and IAM user, as an AWS identity, you can set permission policies to define what another identity associated with them can and cannot do on your bucket. In addition to that, an IAM role provides temporary security credentials which the Platform automatically renews when the user’s bucket is accessed through the Platform, thus increasing the security of the established connection. Learn more.
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.