Workflows
An overview of the workflows in OpenPipelines
Workflows
| Name | Namespace | Description |
|---|---|---|
| BD Rhapsody | Workflows/ingestion | A generic pipeline for running BD Rhapsody WTA or Targeted mapping, with support for AbSeq, VDJ and/or SMK. |
| Bbknn leiden | Workflows/integration | Run bbknn followed by leiden clustering and run umap on the result. |
| Cell Ranger mapping | Workflows/ingestion | A pipeline for running Cell Ranger mapping. |
| Cell Ranger multi | Workflows/ingestion | A pipeline for running Cell Ranger multi. |
| Cell Ranger post-processing | Workflows/ingestion | Post-processing Cell Ranger datasets. |
| Conversion | Workflows/ingestion | A pipeline to convert different file formats to .h5mu. |
| Demux | Workflows/ingestion | A generic pipeline for running bcl2fastq, bcl-convert or Cell Ranger mkfastq. |
| Dimensionality reduction | Workflows/multiomics | Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP. |
| Gdo singlesample | Workflows/gdo | Processing unimodal single-sample guide-derived oligonucleotide (GDO) data. |
| Harmony leiden | Workflows/integration | Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result. |
| Make reference | Workflows/ingestion | Build a transcriptomics reference into one of many formats |
| Process batches | Workflows/multiomics | This workflow serves as an entrypoint into the ‘full_pipeline’ in order to re-run the multisample processing and the integration setup. |
| Process samples | Workflows/multiomics | A pipeline to analyse multiple multiomics samples. |
| Prot multisample | Workflows/prot | Processing unimodal multi-sample ADT data. |
| Prot singlesample | Workflows/prot | Processing unimodal single-sample CITE-seq data. |
| Qc | Workflows/qc | A pipeline to add basic qc statistics to a MuData |
| Rna multisample | Workflows/rna | Processing unimodal multi-sample RNA transcriptomics data. |
| Rna singlesample | Workflows/rna | Processing unimodal single-sample RNA transcriptomics data. |
| Scanorama leiden | Workflows/integration | Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result. |
| Scvi leiden | Workflows/integration | Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result. |
| Split modalities | Workflows/multiomics | A pipeline to split a multimodal mudata files into several unimodal mudata files. |
| Totalvi leiden | Workflows/integration | Run totalVI integration followed by neighbour calculations, leiden clustering and run umap on the result. |
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