OpenPipeline Spatial

Extensible spatial single cell analysis pipelines for reproducible and large-scale spatial single cell processing using Viash and Nextflow.

OpenPipeline Spatial extends the OpenPipeline ecosystem with specialized workflows and components for spatial transcriptomics analysis. It provides standardized, reproducible pipelines that are technology-agnostic and can be used for processing spatial omics data from various technologies and platforms.

Functionality

OpenPipeline Spatial executes a list of predefined tasks specifically designed for spatial omics data. These discrete steps are also provided as standalone components that can be executed individually with a standardized interface.

The following spatial-specific workflows are provided:

• Ingestion: Whereas many technologies generate count matrices on-instrument, functionality is provided for the mapping & quantification of 10X Visum data.
• Interoperability: To make sure all spatial workflows are technology-agnostic, functionality is provided to convert count matrices from different technologies (e.g. Xenium, CosMx, AtoMx, Aviti) into a common format (H5MU). In addition, functionality is provided to convert between various Spatial data formats (e.g. Seurat, SpatialExperiment, MuData, SpatialData).
• QC: Calculation of comprehensive quality control metrics.
• Sample Processing: Batch processing of multiple spatial samples, including count-based filtering, normalisation and dimensionality reduction.

Extended functionality

Whereas this package only provides spatial-specific functionality, it is designed to work seamlessly with the core OpenPipeline package. This means that all core OpenPipeline workflows and components can be used in conjunction with the spatial-specific ones. For example, the integration and cell type annotation workflows can be applied to spatial data after it has been processed using the spatial-specific workflows.

flowchart LR
  demultiplexing["Step 1: Ingestion"]
  ingestion["Step 2: QC"]
  process_samples["Step 3: Process Samples"]
  integration["Step 4: Integration"]
  downstream["Step 5: Downstream Analysis"]
  demultiplexing-->ingestion-->process_samples-->integration-->downstream

Execution via CLI or Seqera Cloud

The openpipeline_spatial 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 launch button.
• Select the execution environment of choice (e.g. Seqera Cloud, CLI or Executable)
• Fill in the form with the required parameters and launch the workflow.

Support

For issues specific to spatial analysis, please use the GitHub issues tracker. For general OpenPipeline questions, refer to the main OpenPipeline documentation.