Release notes

May 31st, 2021

SB CLI now accepts automation start parameters as YML or JSON file

Starting from SB CLI version 0.18.0, arguments necessary for initiating a new automation run via the automations CLI can come from inside a user-provided YML or JSON file. 

This allows you to maintain automation parameters inside well organized and annotated file templates, instead of providing all arguments (in particular automation inputs, settings, and secret settings) in the form of a long, opaque command line string that is difficult to read and write.

When starting a new automation, you would first need to modify the local YML/JSON file and then provide the file path as an argument to the sb automations start command. Read more on the Manage via CLI RHEO documentation page.

GDC Datasets version update

As of May 27, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 29.0.

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May 24th, 2021

New Command-line Uploader released

The new Command-line (CLI) Uploader, just released as part of the existing Seven Bridges CLI tool, becomes the primary recommended tool for performing large scale uploads to the Seven Bridges Platform. The Uploader is easy to install and use, and is a resilient and performant command line application that provides users with a secure and reliable way of uploading data to the Platform.

The legacy Command line uploader will remain functional until August 2021, before being officially deprecated. Along with the legacy CLI Uploader, Desktop Uploader is also planned to be deprecated in August 2021, as Web Uploader is available through the Platform’s visual interface (since September 2020). Find out more about the new CLI Uploader in our documentation.

Recently published apps

GENESIS Update Null Model for Fast Score Test updates null model file obtained with the GENESIS Null model workflow so that it can be used in the GENESIS Single Variant Association Testing workflow in fast score mode.

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May 17th, 2021

CWL v1.2 available on the Seven Bridges Platform

Seven Bridges Platform now supports Common Workflow Language (CWL) version v1.2. The new version of CWL brings a major new functionality – conditional execution of workflow steps, as well as several minor features and improvements. For the detailed change log please see the CWL CommandLineTool specification and the CWL Workflow specification.

The new CWL version v1.2 is a backwards-compatible upgrade of version v1.1, meaning all v1.0 and v1.1 features are still supported in v1.2. To upgrade a v1.0 or v1.1 app to v1.2, simply edit the app and the next version you save can automatically be upgraded to v1.2. Note that upgrading a workflow CWL version to v1.2 this way will not upgrade the CWL version of the tools in the workflow.

Apps using CWL v1.0 and v1.1 versions are still supported and can be used in workflows in combination with CWL v1.2 apps.

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April 26th, 2021

Recently published apps

The following apps were published in CWL1.x:

  • SRA Toolkit 2.10.8 – NCBI’s collection of tools and libraries for accessing data in Sequence Read Archives format (SRA).
  • SRA Download and Set Metadata a workflow that allows for downloading full SRA datasets and populating any metadata information that goes with the dataset
  • AnnotSV 3.0.7 – structural variant annotation and raking tool.
  • IsoformSwitchAnalyzeR 1.12.0 – a tool for differential splicing analysis, it performs statistical identification of the isoform switching while comparing two sample groups.
  • DRIMSeq 1.16.1 – performs differential transcript usage (DTU) analyses using Dirichlet-multinomial generalized linear models.
  • DEXSeq 1.36.0 – toolkit for testing differential exon usage in comparative RNA-Seq experiments.
  • Differential Exon Usage with DEXSeq 1.36.0 – a workflow constructed out of DEXSeq tools, meant for a comprehensive differential splicing analysis.
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April 19th, 2021

Recently published apps

The following apps were published in CWL1.x:

  • Single Cell Multi Sample Pairwise Differential Expression Workflow – pipeline that performs differential expression analysis on single cell data between pairs of user defined conditions.
  • Minimap2 v2.17 – a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database, tailored for use with long read sequencing technologies.
  • fastqValidator 0.1.1 – checks format correctness of paired-end and single-end FASTQ files.
  • FastP 0.20.1 – ultra-fast FASTQ preprocessor with useful quality control and data-filtering features, including adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of FASTQ data.
  • SBG convert SRA/BAM to FASTQ – an all-in-one tool that converts SRA/SAM/BAM/CRAM files into FASTQ format.
  • SBG Create Expression Matrix – creates aggregated matrices from various types of inputs, most typically from abundance estimates produced by tools like RSEM, Salmon, or Kallisto.
  • SHAPEIT 4.2.1 – phasing tool for sequencing and SNP array data.
  • Regenie 2.0.1 – tool for whole genome regression analysis.
  • UMI-tools 1.1.1 – tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
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April 12th, 2021

Recently published apps

MaxQuant is a tool for quantitative proteomics, designed for analysing large mass-spectrometric data. It takes files with high-resolution, quantitative MS data and produces information about quantification of proteins and PTMs. It can be used for analysing data derived from any major relative quantification techniques (Label-free quantification (LFQ), MS1-level labelling and isobaric MS2-level labelling). Furthermore, it provides quantification algorithms for all common forms of tandem mass (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ) labelling (including higher-plex TMT and multinotch MS3 quantification).

GENESIS Association Results Plotting creates Manhattan and QQ plots from GENESIS association test results with additional filtering and stratification options available. This app with it’s default options is the part of a GENESIS Association testing workflows, however after the association testing is completed users can fine-tune the Manhattan and QQ plots by running this app separately.

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April 5th, 2021

Recently published apps

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

  • GATK
  • Picard
  • VEP toolkit and workflow
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March 22nd, 2021

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.

 

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March 8th, 2021

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.

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