Release notes

Recently published apps

We’ve just published AnnotationDbi select and mapIds, a tool that maps one type of IDs to another. It is based on Bioconductor annotation data packages.

Recently published apps

New apps have been added to the Seven Bridges Platform:

• Two tools from the Samplot toolkit:
  • Samplot Plot takes alignment files and coordinates for a region containing the SV call of interest (Chromosome, Start position, and End position) and creates a plot of the SV region.
  • Samplot Vcf can be used to create visualizations of structural variant calls from a VCF file.
• Seven tools from the Smoove toolkit:
  • Smoove Annotate annotates SV calls with SV quality and gene information from GFF3 files.
  • Smoove Call calls structural variants with Lumpy and optionally calls svtyper.
  • Smoove Duphold annotates SV calls in the file based on information from the provided alignment files.
  • Smoove Genotype runs svtyper in parallel on provided SV inputs.
  • Smoove Merge merges SV calls from individual files with SV calls and sorts them using svtools.
  • Smoove Paste squares matching SV calls from individual files to a single joint file with final calls.
  • Smoove Plot-counts takes a VCF file created by other Smoove tools and plots counts of split and discordant reads before and after filtering.
• Upgraded four Sambamba tools to 0.8.1 (and CWL 1.2) and added three new tools:
  • Sambamba Flagstat generates statistics from read flags in a BAM file.
  • Sambamba Index creates a BAI or FAI index for the provided input.
  • Sambamba Markdup can be used to mark or remove duplicate reads from an input BAM file.
  • Sambamba Merge merges alignments in BAM format.
  • Sambamba Slice can be used to copy a slice (region) of the coordinate sorted and indexed input file in BAM or FASTA format.
  • Sambamba Sort sorts alignments in BAM format.
  • Sambamba View accepts alignments in BAM or SAM format and outputs data in a user-specified format.
• Vcf2maf is a tool that converts VCF files to MAF files. To obtain a MAF file from a VCF, each variant must be mapped to exactly one gene transcript/isoform that it might affect, and be associated with exactly one effect. Vcf2maf invokes Variant Effect Predictor to choose the transcript and effect associated with each variant in the output MAF file.
• Cancer Predisposition Sequencing Reporter tool that can be used to interpret germline variants in the context of cancer predisposition. The tool takes a VCF file with germline variants obtained from WES or WGS, cross-references the set with the user-selected set of genes of interest, annotates the variants and reports the associated information (ClinVar-classified variants, ACMG secondary findings, Variant biomarkers and GWAS hits).
• Personal Cancer Genome Reporter can be used to analyze a VCF with somatic variants obtained using WES, WGS or targeted sequencing. It is a tool for functional annotation and classification of somatic variants.
• Whole Genome Sequencing – Quality Control workflow, used for quality control of WGS data. The workflow is intended as a general-purpose QC workflow for users processing WGS data, offering plots which can be easily inspected, as well as structured data output suitable for aggregation and parsing in an automated setup (JSON and TAR.GZ archive with all QC files).

GDC Datasets version update

As of March 11, 2022, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 31.

Recently published apps

We have added four apps to our public apps gallery:

• Single cell RNA-seq velocity analysis with scVelo 0.2.4 workflow that performs preprocessing, marker gene analysis, and velocity analysis of single-cell expression data. It is based on SingleCellExperiment, Seurat, scran, scater, AnnotationHub, scuttle, and scVelo.
• Velocyto.py – Velocyto 0.17.17 is a package for the analysis of expression dynamics in single cell RNAseq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Velocyto.py is a command line tool (distributed with the package) that is used to generate spliced/unspliced count matrices.
• SBG single cell object convertor tool that performs conversion of single cell data object type for commonly used formats: Seurat, AnnotatedData, and SingleCellExperiment.
• Single cell RNA-seq trajectory analysis with slingshot and tradeSeq, a tool that performs single cell trajectory analysis with slingshot 2.0.0, and differential expression testing on inferred trajectories with tradeSeq 1.6.0. Slingshot takes advantage of single cell data principal components analysis (PCA) and clustering to infer probable paths of cell development.

NewSupport for Nextflow and WDL workflows available on the Seven Bridges Platform

Apart from significant contributions from Seven Bridges team members to the development of the Common Workflow Language (CWL) and its extensive implementation on our Platform, we are now taking a step further and providing support for two more workflow description languages, Nextflow and WDL. This presents a groundbreaking move in the direction of enabling you to reduce the time needed to bring your apps to the Seven Bridges Platform, eliminate the need for conversion of your Nextflow or WDL code, while still allowing you to use a better interface for running workflows and all other out-of-the-box features in the Seven Bridges ecosystem. 

The process of bringing Nextflow and WDL apps to the Seven Bridges Platform is designed to be in line with the existing app development tools and practices and is a matter of using the existing Nextflow and WDL code, making configuration optimizations to get the maximum out of the Seven Bridges execution environment and using the sbpack utility to help with the optimization and the actual communication with the Seven Bridges Platform. To guide you through the process, the documentation describes the process for both Nextflow and WDL workflows.

This implementation is the initial release and will be under intensive development in the future. Further improvements will include performance improvements, such as the capability of running different parts of a Nextflow or WDL workflow on different compute instances, as well as many others that will significantly contribute to a better user experience.

ImprovementsRHEO – improved scaling and more elastic execution infrastructure

We have improved our automation execution infrastructure by enabling it to scale up its compute capacity automatically when there is an increased workload and a need for new automation runs to be initialized. In addition, we have introduced a limit of 30 parallel automation runs per Division as a measure of precaution to ensure proper use of the elastic automation execution service. Executions that require more than 30 parallel runs are still absolutely possible, as the limit can be increased if there is an actual need for more capacity. Please contact support@sevenbridges.com for more details.

AWS i3 instances available on all environments

With this update you can use the newest Amazon EC2 I3 instances designed for data-intensive, high transaction, low latency workloads, offering the best price per I/O performance (I3) and the lowest price per GB of SSD instance storage on Amazon EC2 (I3en).

The following instances have been added:

• i3.large
• i3.xlarge
• i3.2xlarge
• i3.4xlarge
• i3.8xlarge
• i3.16xlarge
• i3en.large
• i3en.xlarge
• i3en.2xlarge
• i3en.3xlarge
• i3en.6xlarge
• i3en.12xlarge
• i3en.24xlarge

Learn more about supported AWS instance types.

Recently published apps

We have published GATK RNAseq short variant discovery 4.2.0.0 workflow, which represents a CWL implementation of the official GATK best practices workflow given in WDL for RNASeq variant discovery. Starting from an unmapped BAM file, the workflow performs alignment to the reference genome, followed by marking of duplicates, reassigning of mapping qualities, base recalibration, variant calling, and variant filtering.

NewRecently published apps

We have published 10 tools from the GRIDSS module software suite (toolkit) containing tools useful for the detection of genomic rearrangements:

• GRIDSS tool, a structural variation caller for Illumina sequencing data. It calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
• GRIDSS Extract Overlapping Fragments is used to extract reads of interest for targeted GRIDSS variant calling.
• GRIDSS Annotate VCF Kraken2 adds Kraken2 classifications to single breakend and breakpoint inserted sequences.
• GRIDSS Annotate VCF RepeatMasker adds RepeatMasker classifications to inserted sequences.
• GRIDSS GeneratePonBedpe aggregates variants from multiple VCFs and counts the number of samples supporting each.
• GRIDSS SetupReference is used for generating additional files for the reference needed for running GRIDSS.
• GRIDSS Somatic Filter filters somatic calls from a VCF generated by GRIDSS joint tumor/normal variant calling.
• GRIDSS VIRUSBreakend is a high-speed viral integration detection tool. It is designed to be incorporated in the WGS pipelines with minimal additional cost.
• GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output. It produces a high confidence set of somatic SV for a tumor sample.
• GRIPSS Hard Filter applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output. It produces a high confidence set of somatic SV for a tumor sample.

Recently published apps

We’ve just published OlinkAnalyze DE, a tool that performs differential expression analysis on Olink Normalized Protein eXpression (NPX) data, and OlinkAnalyze QC that generates a quality control and exploratory analysis report on Olink NPX data.

SBFS support for macFUSE 4.x

SBFS is a command-line tool which enables interaction with Platform project files that are mounted as a local file system. In order to use SBFS, it is necessary to have the FUSE component installed. While FUSE is a part of the Linux kernel, on macOS it is necessary to install FUSE for macOS (which is now called macFUSE) and we are now adding support for macFUSE version 4.x (macFUSE 4.0.0 was released in October 2020, and that is when the name was changed from “FUSE for macOS” to “macFUSE”, while its latest version is macFUSE 4.2.4). Please note that SBFS is available as a BETA tool. Also, it’s not available for the Windows operating system, but only for Linux and macOS.

Data throughput usage dashboard now available for Enterprise

As an Enterprise Administrator or Division Administrator, you are able to review the data throughput either for the whole Enterprise or for individual divisions and for the desired time interval (e.g. weeks or months or the whole year). Files used in tasks, files used in Data Cruncher analyses and data downloads are included in the Data Throughput calculation.

As of January 1st 2022, Data Throughput only takes into account files that are used by the tools in a task (as opposed to files set as inputs to a task). Furthermore, data downloaded from the Internet by tasks and Data Cruncher analyses is also included in the calculation. Learn more about reviewing Enterprise data throughput.

Data Cruncher default environment update

The default environment for Data Cruncher interactive analyses has been updated to include more up-to-date versions of Python (upgraded to 3.9) and R (upgraded to 4.1). 

GDC Datasets version update

As of December 17, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 30.0.