Key features
Modular
Reusable components built with Viash for flexible pipeline construction.
Scalable
Leverage Nextflow for execution on various platforms (local, cloud, HPC).
Reproducible
Containerized components and unit testing ensure reliable analyses.
Collaborative
A framework for sharing and integrating components to foster teamwork.
Living Best Practices
Adapts to evolving single-cell analysis by incorporating current best practices and novel methods.
Multimodal
Supports diverse single-cell data types (RNA, protein, VDJ, ATAC) for multi-omics analyses.
Overview
flowchart LR
%% Ingestion
subgraph ingestion[Step 1: Ingestion]
direction LR
10x_ingestion[10x Ingestion]:::subwf
bd_ingestion[BD Rhapsody\nIngestion]:::subwf
own_h5mu[Own H5MU]:::subwf
end
ingestion:::info
%% Process samples
subgraph process_samples[Step 2: Process Samples]
direction LR
gex[GEX]:::subwf
atac[ATAC]:::subwf
adt[ADT]:::subwf
vdj[VDJ]:::subwf
other[Other]:::subwf
end
process_samples:::info
%% Integration and downstream
subgraph integration[Step 3: Integration]
direction LR
harmony[Harmony]:::subwf
scvi[scVI]:::subwf
scanvi[scanVI]:::subwf
etc[...]:::subwf
end
integration[Integration]:::info
subgraph downstream[Step 4: Downstream]
direction LR
celltype_annotation[Cell Type\nAnnotation]:::subwf
markergenes[Marker Genes\nAnalysis]:::subwf
differential[Differential\nExpression]:::subwf
gene_signature_analysis[Gene Signature\nAnalysis]:::subwf
ccc[Cell-Cell\nCommunication]:::subwf
end
ingestion --> process_samples --> integration --> downstream
classDef wf fill:#f0f0f0,stroke:#525252
classDef subwf fill:#d9d9d9,stroke:#525252
classDef info fill:#f0f0f0,stroke:#525252,stroke-dasharray: 4 4