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

License: MIT License

Shell 0.11% Python 70.27% CSS 0.12% Makefile 0.56% Batchfile 0.67% Jupyter Notebook 16.58% Dockerfile 0.73% Nextflow 10.96%

webatlas-pipeline's Introduction

WebAtlas Pipeline

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

A parameters file looks like:

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:

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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