Development Release Notes (March 15, 2022)

On March 15, 2022, the All of Us Researcher Workbench team released the new Controlled Tier dataset. Throughout the Alpha Testing phases, the team found and fixed bugs, tweaked and improved features, and utilized demonstration project team feedback to further elevate the Workbench. In the last phase of Alpha testing, the following changes were implemented:

Bug Fixes

• Increased the values offered for user credits.
• Added better cost visibility when recreating analysis environments with your last-known configuration

Genomic Data

• We now have included the following files:
• 98,622 Whole Genome Sequencing (WGS) VCF files
• WGS auxiliary (sample QC / relatedness / genetic ancestry) files
• WGS hail matrix table
• 165,208 Microarray VCF files
• Microarray Hail matrix table
• Microarray PLINK files (bed / bim / fam)
• Please note that all variants are called against the hg38/GRCh38 reference.  

Features

• Spark Console UI links now available from the Cloud Analysis panel, helpful in debugging Hail / Spark failures or monitoring Hail / Spark jobs
• Notebook image improvements, added the following tools:
• plink2
• GCTA
• vcftools
• PRSice
• Initial batch processing support
• Cromwell
• Nextflow
• dsub

Resources

• Controlled Tier training is now available in the registration process
• We have created a Featured Workspace to demonstrate how to more easily execute long-running computations in the notebook environment.
• To help users better understand how to navigate a cloud-based platform, we have developed multiple support sources based on your feedback. Look for the Featured Workspace “How to work with the All of Us Genomics Data (Hail+PLINK)” that will guide you through a ready-to-use Hail matrix table.
• We have added three tutorial workspaces to introduce batch processing: “How to run WDLs with Cromwell in the Researcher Workbench”, “How to use Nextflow in the Researcher Workbench” and “How to use dsub in the Researcher Workbench”

Pending Features Functionalities 

• Dataset builder genomic VCF extraction updated for Alpha 3

To our demo users, we want to thank you for all you have done to prepare us for this Controlled Tier and Genomics launch. Your patient endurance through finding bugs, learning a new coding language, managing this project on top of other work, and showing up to office hours does not go unnoticed. Your work has been pivotal for us and fellow researchers using the Researcher Workbench. Thank you for helping us get to where we are today and where we are headed in the future!