Release notes

NewAccess task secondary files via the API

You can now use our sevenbridges-python client to access secondary files for task inputs and outputs.

New and improved functionality:

1. API users can now see exactly which files were used as secondary files for inputs.
2. Python client can now easily get those files via a simple call, as shown in the example below.
3. All of this is also supported for CWL 1.x tools and workflows, where the secondary files can be defined as JS expressions.

Some examples utilizing the sevenbridges-python API client:

import sevenbridges as sb
config = sb.Config(profile='default')
api = sb.Api(config=config)

task = api.tasks.get('439221a0-27c8-47a3-bcac-fcc5f44f82a8')
output_secondary_files = task.outputs['my_output'].secondary_files
input_secondary_files = task.inputs['my_input'].secondary_files
print(output_secondary_files)
print(input_secondary_files)

Please note that secondary files are captured from tasks as inputs or outputs, not from the file system. This means that the secondary_files property is available only when the file is pulled from the task itself, not when it is reloaded from the file system or directly instantiated from the file system via the api.files.get(<FILE_ID>) call or a similar one. The only supported way of getting secondary files is shown above – they need to be captured as soon as possible from the input file.

Learn more about the sevenbridges-python API client.

Whole Genome Sequencing – Quality Control – CWL1.0 Workflow

Data quality control (QC) is an important component of NGS projects, especially with relatively costly whole genome sequencing (WGS). Timely QC can identify and account for issues with the starting biological material (DNA contamination or sample swaps), the sequencing process or bioinformatic pipelines used for processing.

Whole Genome Sequencing – Quality Control – CWL1.0 Workflow is intended as a general-purpose QC flow for users processing WGS data, regardless of the number of samples. It should offer plots which can be easily visually inspected by the end users, as well as structured data output suitable for aggregation and parsing in an automated setup. As it may be of interest to keep the cost and duration of single-sample tasks to a minimum in large-scale sequencing projects, the workflow is designed to be modular, with nodes that can be turned on/off on request, or segments completely skipped (based on input data availability, for example).

ReleaseGDC Datasets version update

As of August 7, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 18.

New and improved API calls for user management

You will be able to use new and improved API calls for enterprise users that enable you to:

1. List all users from a division with filtering based on the role field,
2. Get role information for a user in a division,
3. List all teams, not only the ones you are a member of.

The changes will enable you to create various API scripts to answer questions like:

• Who has access to what?
• How much money was spent on compute per team?
• Do I have some external collaborators on my enterprise that I forgot about?

Some examples utilizing the sevenbridges-python API client:

(more…)

ReleaseGDC Datasets version update

As of July 10, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 17.

ReleaseCPTAC-3 data release

With this release we will have controlled access data from the CPTAC-3 project available on the Platform for search and filtering in the Data Browser and through the API. This set contains WGS, WXS, and RNA-Seq data that is protected, and access to it requires approval from dbGaP. The data has been collected within the CPTAC (Clinical Proteomic Tumor Analysis Consortium) program, in the third phase labelled as CPTAC-3. The program was focused on collection of proteomics data for patients with a particular cancer type, but the data collection is also expanded to genomic data, particularly for lung, kidney, and uterus carcinoma. The primary source for this genomic data is at the GDC. Read more.

Supported browsers update

Internet Explorer is no longer a supported browser on the Seven Bridges Platform. When trying to access the Platform using Internet Explorer, you will be presented with an adequate explanatory message stating that you are using an unsupported browser and suggesting that you switch to a supported one.

We have also updated the minimum required versions for the supported browsers:

• Google Chrome 72.0.3626 (2019-01-29)
• Mozilla Firefox 60.5esr (2019-01-28)
• Apple Safari 12.0 (2018-09-17)
• Opera 58 (2019-01-23)
• Microsoft Edge 44.17763 (2018-11-13)

Recently published apps

The following apps have been ported to CWL 1.0 and are now available as CWL 1.0 apps in the Public Apps gallery:

• Optitype 1.2
• VEP annotation workflow 90.5
• Ensembl-VEP 90.5

Writing rate limit-efficient API scripts

The API rate limit is a limit to the number of calls you can send to the Seven Bridges API within a predefined time frame. That limit is 1,000 requests within 5 minutes. After this limit is reached, no further calls are accepted by the API server until the 5 minute interval ends.

It is important to write API scripts with this API rate limit in mind to minimize the number of API calls to the Seven Bridges Platform. This way, you avoid reaching your rate limit and your API scripts can execute without delay due to server-side throttling.

We put new documentation online that helps you make your API scripts rate limit-efficient. Code snippets demonstrate recommended use of the Seven Bridges Python client to minimize API calls for common tasks, including finding projects, iterating over result sets of queries, importing files from volumes, exporting files to volumes, updating file metadata, copying files between projects, deleting files, and submitting tasks for execution.

If you ever experienced errors or delays due to the Seven Bridges API rate limit, please make sure to give this new content a read to learn how to make your API calls (not) count.

NewSeven Bridges Automation Tools and Services

The new Seven Bridges Automation Tools and Services enable biotechnology and biopharmaceutical companies to increase productivity by bringing a diverse set of users into one environment. Scripts written with the Python Automation Development Kit (ADK) automatically gain concurrency, dependency management, memoization, retries, execution logs, and much more, enabling developers to focus on business logic and ultimately, reduce their lines of code by up to 80%. Within the same environment, end users are now able to process complex analysis workflows with the push of a button, share results instantly, and achieve total reproducibility.

Visit sevenbridges.com/automation for more details.

Supported instances update

You can now use next generation AWS Memory Optimized instances (R5) in task executions and Data Cruncher analyses. R5 instances support the high memory requirements of certain applications to increase performance and reduce latency.

Learn more about supported instance types.