Merge pull request #9 from openpipelines-bio/readme

Readme

Author: dorien-er

CHANGELOG.MD

@@ -1,3 +1,9 @@
+# openpipeline_qc x.x.x
+
+## MINOR CHANGES
+
+* Add a README (PR #9).
+
 # openpipeline_qc 0.1.0
 
 Initial release containing a QC Reporting workflow for Xenium or CellRanger Multi ingested data, with corresponding components.

README.md

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+# OpenPipeline QC
+
+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](https://github.com/openpipelines-bio/openpipeline/) ecosystem and extends it with specialized functionality for ingestion quality control.
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-openpipeline_qc-7a4baa.svg)](https://www.viash-hub.com/packages/openpipeline_qc)
+[![GitHub](https://img.shields.io/badge/GitHub-openpipelines--bio%2Fopenpipeline_qc-blue.svg)](https://github.com/openpipelines-bio/openpipeline_qc)
+[![GitHub License](https://img.shields.io/github/license/openpipelines-bio/openpipeline_qc.svg)](https://github.com/openpipelines-bio/openpipeline_qc/blob/main/LICENSE)
+[![GitHub Issues](https://img.shields.io/github/issues/openpipelines-bio/openpipeline_qc.svg)](https://github.com/openpipelines-bio/openpipeline_qc/issues)
+[![Viash version](https://img.shields.io/badge/Viash-v0.9.3-blue.svg)](https://viash.io)
+
+## Functionality
+
+### 1. QC Metrics Calculation
+
+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.
+
+### 2. Interactive Report Generation
+
+After calculating QC metrics, the workflow generates a standalone interactive report using the [siqc](https://github.com/openpipelines-bio/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
+
+### 3. Quality Assessment for Downstream Processing
+
+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](https://github.com/openpipelines-bio/openpipeline/) of [OpenPipeline Spatial](https://github.com/openpipelines-bio/openpipeline_spatial/) packages.
+
+**Supported platforms:**
+- 10x Genomics single-cell multi-omics (Cellranger Multi output)
+- 10x Genomics Xenium spatial transcriptomics
+
+## Execution via CLI or Seqera Cloud
+
+The openpipeline_qc package is available via [Viash Hub](https://www.viash-hub.com/packages/openpipeline_qc/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_qc/-/tree/build/main/target/nextflow/workflows/generate_qc_report) 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_qc/latest/), select the workflow you want to launch and click the `launch` button.
+* Select the execution environment of choice (e.g. `Seqera Cloud`, `Nextflow` or `Executable`)
+* Fill in the form with the required parameters and launch the workflow.
+
+## Support
+
+For issues specific to quality control analysis, please use the [GitHub issues tracker](https://github.com/openpipelines-bio/openpipeline_qc/issues). For general OpenPipeline questions, refer to the main [OpenPipeline documentation](https://openpipelines.bio/).