Release Note
Recently published apps and resources
This release expanded the availability of key scientific workflows and upgraded QIIME2 workflows for microbiome research and STAR-based tools for RNA-seq analysis. These updates were designed to improve reproducibility, usability, and accessibility for researchers working across genomics, imaging, and multi-omics workflows.
Enhancements to the Nextflow import application
Several improvements were delivered to the sbpack_nf CWL App to streamline onboarding and deployment of Nextflow workflows on Seven Bridges platform, including:
- Support for importing Nextflow workflow packages directly from public GitHub repository URLs, reducing the need for manual archive uploads.
- Validation checks to prevent unsupported string output types during workflow packaging. Improved compatibility with EPI2ME and nf-core workflows
Together, these updates improve workflow portability, reduce deployment errors, and simplify the packaging process for Nextflow users on the platform.
Single-Cell Analysis Resources
A standardized Monocle workflow has been developed to support scalable and reproducible single-cell RNA-seq trajectory analysis. This workflow enables researchers to:
- Reconstruct developmental and cellular trajectories.
- Perform pseudotime analyses.
- Explore branching lineage relationships.
- Investigate gene expression changes associated with cell state transitions.
By providing a configurable and reusable workflow, this release simplifies advanced single-cell trajectory analysis for a broad range of biological applications.
Microbiome Analysis Improvements
The publicly available QIIME2 workflows for microbiome analysis have been reviewed, updated, and validated to align with current platform standards. Updated workflows include:
- 16S rRNA Feature Classifier Training
- 16S rRNA Metagenomic Profiling
- QIIME2 Core Diversity Reporting
Improvements include workflow validation, refreshed configurations, updated parameter guidance, enhanced documentation, and verification of referenced assets and metadata. These updates help ensure reliable execution and a more consistent user experience for microbiome researchers.
RNA-seq Workflow Updates
The STAR toolkit and associated RNA-seq alignment workflows available through the Public Apps Gallery have been updated to the latest supported version, improving consistency and maintaining alignment with current platform standards. The update includes the following components: STAR, STARsolo, STARsoloCellFiltering, STAR Genome Generate, and the RNA-seq Alignment STAR workflow. This release ensures that users performing bulk and single-cell RNA-seq analyses have access to the most up-to-date STAR-based tools while maintaining compatibility with existing analysis workflows. The refreshed toolkit supports reliable sequence alignment, genome indexing, and single-cell transcriptomic preprocessing across a variety of RNA-seq applications.
Resources
If you have questions or need help with any of these new resources, please contact your Velsera Seven Bridges representative or email support@velsera.com.
