OpenPipeline QC contains an extensible workflow for the generation of a stand-alone, interactive ingestion QC report for single-cell and spatial omics data. It is part of the OpenPipeline ecosystem and extends it with specialized functionality for ingestion quality control.
The workflow calculates extensive ingestion QC metrics at both the observation and feature levels. Observation-level metrics include total counts per cell, gene detection rates, mitochondrial and ribosomal gene percentages, and expression concentration in top genes. Feature-level metrics cover gene expression summaries such as total counts per gene, detection rates across cells, mean expression levels, and dropout percentages.
Spatial data metrics: For spatial data, the workflow also surfaces segmentation metrics.
After calculating QC metrics, the workflow generates a standalone interactive report using the siqc package (standalone, interactive QC reporting engine).
siqc features:
- 🚀 Progressive Loading: Large datasets (millions of cells) load incrementally without blocking the UI
- 📊 Interactive Visualizations: Histograms, scatter plots, heatmaps, and spatial plots with Plotly.js
- 🗜️ Efficient Compression: Binary data format with gzip compression for optimal file sizes
- 📄 Standalone Reports: Single HTML file with no external dependencies
- 🎯 Spatial Analysis: Advanced spatial plotting with faceting and optimization
- ⚡ Performance Optimized: Web Workers, typed arrays, and multi-scale rendering
The generated report can be used to set thresholds for QC-based filtering, which can then be applied for further processing of the data using the core OpenPipeline of OpenPipeline Spatial packages.
Supported platforms:
- 10x Genomics single-cell multi-omics (Cellranger Multi output)
- 10x Genomics Xenium spatial transcriptomics
The openpipeline_qc package is available via Viash Hub, where you can receive instructions on how to run the end-to-end workflow as well as individual subworkflows or components.
It's possible to run the workflow directly from Seqera Cloud. The necessary Nextflow schema files have been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters for batch processing of multiple samples. Therefore, it's better to use Viash Hub also here for launching the workflow on Seqera Cloud.
- Navigate to the Viash Hub package page, select the workflow you want to launch and click the
launchbutton. - Select the execution environment of choice (e.g.
Seqera Cloud,NextfloworExecutable) - Fill in the form with the required parameters and launch the workflow.
For issues specific to quality control analysis, please use the GitHub issues tracker. For general OpenPipeline questions, refer to the main OpenPipeline documentation.