Introduction Usage Parameters Output

Introduction

This document describes the output produced by the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

Pipeline overview

The pipeline is built using Nextflow and outputs the following information:

SpatialData directory

Output files
  • {sample}.zarr/
    • Spatial elements: images/, shapes/, tables/, points/, …

The {sample}.zarr directory contains a SpatialData object, where the sample name is either (i) specified by the samplesheet, or (ii) based on the name of the corresponding input directory.

Refer to the SpatialData docs for usage details, or to the documentation of sopa as a Python package. If you are not familiar with SpatialData, you can also use directly the extracted AnnData object (see below).

Explorer directory

Output files
  • {sample}.explorer/
    • Sopa quality controls: report.html
    • AnnData object (extracted from the above SpatialData object): adata.h5ad
    • Xenium Explorer file: experiment.xenium. Double-click on it to open it on the Xenium Explorer; you can download the software here.
    • Other files related and required by the Xenium Explorer.

The {sample}.explorer directory can be used for visualization and quick analysis.

VisiumHD-specific outputs

(Only for Visium HD) a {sample}_spaceranger/outs directory with the outputs of Space Ranger. See the official 10X Genomics documentation for more details.

Pipeline information

Output files
  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter’s are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.
    • Parameters used by the pipeline run: params.json.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
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