Release notes

Recently published apps

The following apps were upgraded to CWL1 and had their versions updated as well:

• GATK
• Picard
• VEP toolkit and workflow

GDC Datasets version update

As of March 17, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 28.0.

Recently published apps

• GATK Somatic SNVs and INDELs (Mutect2) 4.1.9.0 can be used to detect SNVs and INDELs in one or more tumor samples from a single individual, with or without a matched normal sample. Assembly implies whole haplotypes and read pairs, rather than single bases, as the atomic units of biological variation and sequencing evidence, improving variant calling.
• GATK Somatic Create Mutect2 Panel of Normals 4.1.9.0 workflow creates a panel of normals (germline and artifactual sites) for use in other GATK workflows. It takes multiple normal sample callsets produced by GATK Somatic SNVs and INDELs 4.1.9.0 (Mutect2 workflow) tumor-only mode (although it is called tumor-only, normal samples are given as the input) and collates sites present in two or more samples into a sites-only VCF.

Both workflows are composed in reference to the official GATK’s WDLs.

ImprovementsImproved project organization with project tags 

In order to improve the organization and findability of projects, project tags have been introduced to the Seven Bridges Platform.

Project Admins can now assign tags to projects via the API or through the visual interface. Such tags can be used for filtering purposes when browsing all projects, for projects categorization, and for general custom organization of projects.

The maximum number of tags for a single project is 15, while the maximum number of characters in a single tag is 36. Learn more.

GDC Datasets version update

As of February 22, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 27.0.

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Recently published apps

The following tools were updated to their latest versions and upgraded to CWL1.x:

• HISAT2-StringTie workflow
• StringTie
• Hisat2
• Trimmomatic
• Tabix
• SBG FASTQ Merge

The following new apps were published, in CWL1.x:

• Exomiser 12.1.0 – tool for prioritizing variants from WES and WGS data.
• VEP Slivar Trios Rare Diseases Analysis workflow – analyzes WES and WGS family variants.
• Clustering and Gene Marker Identification with Seurat 3.2.2 – clustering and gene marker identification analysis starting from gene-cell UMI or read counts.
• xCell 1.3 – tool for cell type enrichment analysis, which takes gene expression data and performs analysis for 64 immune and stromal cell types.
• MBASED 1.18.0 tool – used for performing allele specific expression analysis.
• MBASED workflow – based on the MBASED tool, with added phasing and VEP annotation, the workflow allows for easier running of allele specific expression analysis.
• elPrep 4.1.6 – high-performance tool for preparing SAM/BAM files for variant calling in sequencing pipelines, which can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, calculating and applying base quality score recalibration, etc.
• Kraken2 2.0.9 – taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.
• Bracken 2.5 – uses the taxonomic assignments made by Kraken/Kraken2, along with information about the genomes themselves, to estimate abundance at the species/genus level, or above.
• Metagenomics Profiling with Kraken2 – workflow used for metagenomic classification, abundance estimation and visualization.
• cuteSV 1.0.9 – structural variant discovery tool designed for long read sequences.
• Sniffles 1.0.12b – structural variation caller for PacBio or Oxford Nanopore data.
• NanoPlot 1.33.0 – plotting QC tool for long reads sequencing data.
• goleft IndexCov 0.2.4 – used to quickly (in minutes) assess the coverage distribution (16KB resolution) of a WGS cohort from BAI/CRAI files, or infer sex (by plotting the inferred copy number of sex chromosomes).
• vcfanno 0.3.2 – used to annotate variants with information from VCF, BED or BAM sources.
• vcf2db – converts an annotated VCF file into a Gemini-compatible database.
• Cas-OFFinder 2.4 – tool that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.
• BitMapperBS 1.0.2.3 – toolkit for processing WGBS (whole-genome bisufite) reads from directional protocol.
• MethylDackel 0.5.1 – toolkit for processing BS-seq alignments and extracting per-base methylation metrics from them.
• WGBS Analysis BitMapperBS with MethylDackel workflow – developed for BS-seq reads processing and DNA methylation analyses.
• CRISPResso2 2.0.44 – used for analyzing genome editing experiments (public on academic platforms only).
• SAIGE 0.39 – single-variant association tests for binary traits and quantitative traits.
• PRSice-2 2.3.3 – tool for polygenic risk score (PRS) analyses.
• PheWAS R workflow – can be used to conduct PheWAS analyses.
• ONT WGS Data Processing workflow basic workflow for processing Oxford Nanopore WGS data.

Recently published apps

• GATK Broad Best Practice Variant Calling From uBAM – This workflow presents two different BROAD Best Practice workflows incorporated into one – BAM processing and variant calling.
• Functional Equivalence WGS – This workflow processes WGS data according to the functional equivalence standard.

New password validation rules

In order to maintain a high level of security and prevent unauthorized access to the Seven Bridges Platform, we are introducing password checking against a database of commonly used passwords and those that were compromised in data breaches across the Internet, which is why they are considered unsafe. If the entered password exists in this database, you will need to use a different one. 

Additionally, please note that the entire password validation process takes place within the Seven Bridges infrastructure, which ensures an additional level of security as there are no third-party services involved. This password validation mechanism applies when trying to perform the following actions:

• Sign up for a new account.
• Set up a new password to replace an expired one.
• Change the account password.

ImprovementsTask queueing improvements

We have made the following changes to the task queueing process that should improve the queueing logic and contribute to faster completion of initialized tasks and analyses:

• If you reach your parallel instance limit with running tasks, and there are both tasks and Data Cruncher analyses waiting in the queue, Data Cruncher analyses will be first to execute once instances become available.
• If the parallel instance limit is reached with tasks that are being executed, when an instance becomes available it will first be allocated to running multi-instance or scattered tasks if they need additional instances. If there are no such tasks, the instance will be allocated to other task(s) that are next up in the queue. This will enable faster completion of multi-instance and scattered tasks and help avoid breaks in their execution.

Recently published apps

GENESIS LocusZoom visualizes association testing results using the LocusZoom standalone software. This app is a wrapper around LocusZoom standalone software to enable it to work with outputs of GENESIS association pipelines. The main goal of this app is to visualize results of GENESIS Single Variant Association Test, however regions from sliding window or aggregate tests with p-values below a certain threshold can be displayed in a separate track.

SBG Loci Snapshoter generates screenshots of specific regions across all aligned files provided as inputs. It utilizes the IGV batch functionality to create PNG images of desired loci across multiple samples. The main driver of developing this tool was doing a post-association visualisation of associated variants across a subset of CRAM files used to obtain those variants.

ImprovementsData Cruncher Stability and Usability Improvements

Your experience with Data Cruncher just got better thanks to the following improvements:

• Use the full potential of RStudio as it is now officially out of the BETA stage and its stable release is available in Data Cruncher.
• Maintain full control over your workspace integration capabilities in a more secure environment – your Data Cruncher sessions are now run on a separate domain providing even better security isolation and privacy control of your favorite third-party integrated development environments.
• Have a better insight into your session initialization phase with a more informative loading experience.
• Find your way around with more ease – the top navigation bar provides access to analysis information, control options, documentation and feedback form, while the editor continues to provide native experience in your chosen base environment.
  • Seven Bridges addons for JupyterLab (i.e. the Project Files tab and the Save to project right click option) are now deprecated in favor of a unified and improved experience – delivering a more stable and up-to-date visual interface you’re familiar with.
• Enjoy the cost control capabilities (Suspend time) without getting interrupted – your keyboard and mouse activity in the editor is now monitored as session activity in all available environments.

Check out our documentation pages to find out more about Data Cruncher.