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The OpenScPCA Nextflow workflow

In addition to the OpenScPCA-analysis repository, the Data Lab maintains a separate OpenScPCA-nf repository that holds a Nextflow workflow which we use to generate results from mature OpenScPCA-analysis modules.

As analysis modules are completed, the Data Lab will port the analysis code into the OpenScPCA-nf repository and add it to the Nextflow workflow. To ensure reproducibility, the workflow will run each module in its Docker image.

OpenScPCA-nf workflow results

The Data Lab will run the OpenScPCA-nf workflow on the same schedule as we make OpenScPCA data releases, and/or if there have been sufficient changes to the OpenScPCA-nf workflow to merit re-generating results. We will use the workflow to generate two sets of results for each completed module:

In some cases, you may wish to use results from a completed module in your analysis. For example, you may wish to use cell type labels from a module that performed cell type annotation on a set of ScPCA samples.

You can obtain either of these OpenScPCA results using the provided download-results.py script. Please refer to our documentation on the download-results.py script for more information on its usage.

Note that if you need to use results from a module has not yet been added to the OpenScPCA-nf workflow, you will need to run the module yourself to generate results.