43 lines
3.8 KiB
Markdown
43 lines
3.8 KiB
Markdown
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# OpenPipeline Composed
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OpenPipeline Composed provides a comprehensive meta-workflow that combines multiple stand-alone workflows from the [OpenPipeline](https://github.com/openpipelines-bio/openpipeline/) package. The meta-workflow combines sample processing, batch integration, and cell type annotation into a unified pipeline for single-cell multi-omics data analysis.
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[](https://www.viash-hub.com/packages/openpipeline_composed)
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[](https://github.com/openpipelines-bio/openpipeline_composed)
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[](https://github.com/openpipelines-bio/openpipeline_composed/blob/main/LICENSE)
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[](https://github.com/openpipelines-bio/openpipeline_composed/issues)
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[](https://viash.io)
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## Overview
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The sole purpose of this package is to provide a meta-workflow that orchestrates and combines various stand-alone workflows from the [OpenPipeline](https://github.com/openpipelines-bio/openpipeline/) package. By integrating multiple processing steps into a single workflow, it enables seamless processing from raw data to fully annotated, integrated datasets suitable for downstream analysis and atlas generation.
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## Functionality
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The meta-workflow combines three core OpenPipeline workflows:
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- [**Sample Processing**](https://www.viash-hub.com/packages/openpipeline/latest/components/workflows/multiomics/process_samples): Initial quality control, filtering, and preprocessing
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- [**Batch Integration**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fintegration): Integration using **Harmony** or **scVI** methods
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- [**Cell Type Annotation**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fannotation): Annotation using **scANVI** or **CellTypist** methods
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## Key Features
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- 🔄 **End-to-End Processing**: Complete pipeline from raw data to annotated results
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- 📊 **Atlas Generation**: Create comprehensive atlases from multiple datasets and sources
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- 🔬 **Multi-Modal Support**: Process RNA-seq, ATAC-seq, protein, and spatial data
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- 🎯 **Method Flexibility**: Choose from multiple integration and annotation approaches
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- 🧬 **Reference Integration**: Leverage existing reference datasets for annotation
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## Execution via CLI or Seqera Cloud
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The openpipeline_composed package is available via [Viash Hub](https://www.viash-hub.com/packages/openpipeline_composed/latest/), where you can receive instructions on how to run the end-to-end workflow as well as individual subworkflows or components.
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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.
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* Navigate to the [Viash Hub package page](https://www.viash-hub.com/packages/openpipeline_composed/latest/), select the workflow you want to launch and click the `launch` button.
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* Select the execution environment of choice (e.g. `Seqera Cloud`, `Nextflow` or `Executable`)
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* Fill in the form with the required parameters and launch the workflow.
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## Support
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For issues specific to the composed meta-workflow, please use the [GitHub issues tracker](https://github.com/openpipelines-bio/openpipeline_composed/issues). For general OpenPipeline questions, refer to the main [OpenPipeline documentation](https://openpipelines.bio/).
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