openpipelines-bio · dorien-er · Oct 1, 2025 · Sep 30, 2025 · Sep 30, 2025 · Oct 1, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # openpipeline_spatial x.x.x
 
+## MINOR CHANGES
+
+* Add a README (PR #21).
+
 ## NEW FUNCTIONALITY
 
 * `convert`: Updated multiple components to accept spatial output bundles in .zip format (for CosMx, Xenium and Aviti) as input (PR #19).

diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 openpipelines-bio
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
@@ -0,0 +1,55 @@
+# 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](https://github.com/openpipelines-bio/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.
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-openpipeline_spatial-7a4baa.svg)](https://www.viash-hub.com/packages/openpipeline_spatial)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fopenpipeline_spatial-blue.svg)](https://github.com/openpipelines-bio/openpipeline_spatial)
+[![GitHub
+License](https://img.shields.io/github/license/openpipelines-bio/openpipeline_spatial.svg)](https://github.com/openpipelines-bio/openpipeline_spatial/blob/main/LICENSE)
+[![GitHub
+Issues](https://img.shields.io/github/issues/openpipelines-bio/openpipeline_spatial.svg)](https://github.com/openpipelines-bio/openpipeline_spatial/issues)
+[![Viash
+version](https://img.shields.io/badge/Viash-v0.9.3-blue.svg)](https://viash.io)
+
+## 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](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=mapping): Whereas many technologies generate count matrices on-instrument, functionality is provided for the mapping & quantification of 10X Visum data.
+- [Interoperability](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=convert): 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](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=spatial_qc): Calculation of comprehensive quality control metrics.
+- [Sample Processing](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=spatial_process_samples): 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](https://github.com/openpipelines-bio/openpipeline/). This means that all core OpenPipeline workflows and components can be used in conjunction with the spatial-specific ones. For example, the [**integration**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fintegration) and [**cell type annotation**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fannotation) workflows can be applied to spatial data after it has been processed using the spatial-specific workflows.
+
+``` mermaid lang="mermaid"
+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](https://www.viash-hub.com/packages/openpipeline_spatial/latest/), 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](https://packages.viash-hub.com/vsh/openpipeline_spatial/-/tree/build/main/target/nextflow?ref_type=heads) 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](https://www.viash-hub.com/packages/openpipeline_spatial/latest/), 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](https://github.com/openpipelines-bio/openpipeline_spatial/issues). For general OpenPipeline questions, refer to the main [OpenPipeline documentation](https://openpipelines.bio/).