Introduction

STAPLE is a bioinformatics pipeline for 10X Visium and Visium HD spatial data. Being a simple preprocessing-deconvolution-interaction pipeline it features multiple tools, for reference-based deconvolution and cell-cell interaction analysis. In case of reference-based deconvolution, atlas may be specified as an URL on an S3 location (e.g. CellxGene) or a local file, or matched-scRNA made available.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

First, prepare a samplesheet with your input data that looks as follows: samplesheet.csv, where each row represents a spatial transcriptomics sample, and columns holding sample id, and associated data directories. Any extra columns will be treated as metadata and copied into the meta map.

sample: A unique identifier for the sample.

data_directory: The path to the directory containing the output of the spaceranger pipeline.

expression_profile: Optional reference expression profiles (leave blank if not using) if you have known cell types in your Visium data from matched scRNA (different local path to each scRNA atlas) or a local scRNA atals (same path for each sample). If using a remotely stored atlas (such as CellXGene), rather pass params.ref_scrna and the atlas will be downloaded from the web.

Important

export NXF_SINGULARITY_HOME_MOUNT=true in order to allow matplotlib to write its logs (and avoid related error) if using singularity.

Simple Visium SD run with reference-free deconvolution:

nextflow run break-through-cancer/btc-spatial-pipelines \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR> \
   --deconvolve.bayestme \

Run on Visium SD with local reference atlas specified in the samplesheet:

nextflow run break-through-cancer/btc-spatial-pipelines \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>
   --deconvolve.rctd
   --ref_scrna_type_col cell_type_column_name

Run with Visium HD support and remote reference atlas annotation

nextflow run break-through-cancer/btc-spatial-pipelines \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \ 
   --outdir out \
   --visium_hd 'square_016um' \
   --reference_scrna https://datasets.cellxgene.cziscience.com/d1d90d18-2109-412f-8dc0-e014e8abb338.h5ad

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.