webatlas-pipeline

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webatlas-pipeline

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A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas

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# WebAtlas Pipeline

[![docs](https://img.shields.io/badge/Documentation-online-blue)](https://haniffalab.github.io/webatlas-pipeline)
[![demo](https://img.shields.io/badge/Demos-view-blue)](https://cellatlas.io/webatlas)
[![doi](https://zenodo.org/badge/DOI/10.5281/zenodo.7405818.svg)](https://doi.org/10.5281/zenodo.7405818)

The WebAtlas Pipeline uses Nextflow to process spatial and single-cell experiment data for visualisation in a web browser.

## Usage

The pipeline can handle data from `h5ad` files, `tif` image files, SpaceRanger, Xenium and MERSCOPE output. It can also generate label image files from data files.

Running the pipeline requires a parameters file that defines configuration options and the data to be processed.
Full instructions and parameters definitions for this files are available in the [documentation](https://haniffalab.com/webatlas-pipeline/configuration.html)

A parameters file looks like:

```yaml
outdir: "/path/to/output/"

args:
  h5ad:
    compute_embeddings: "True"

projects:
  - project: project_1
    datasets:
      - dataset: dataset_1
        data:
          - data_type: h5ad
            data_path: /path/to/project_1/dataset_1/anndata.h5ad
          - data_type: raw_image
            data_path: /path/to/project_1/dataset_1/raw_image.tif
          - data_type: label_image
            data_path: /path/to/project_1/dataset_1/label_image.tif

vitessce_options:
  spatial:
    xy: "obsm/spatial"
  mappings:
    obsm/X_umap: [0, 1]
layout: "simple"
```

The pipeline can then be run like:

```sh
nextflow run main.nf -params-file /path/to/run-params.yaml -entry Full_pipeline
```

Parameters file templates are available in the `templates` directory.

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