Updated merged objects are now available in the results bucket

[sjspielman]

As noted in #1183, consensus cell type annotations from the cell-type-consensus analysis module were made available in SingleCellExperiment and AnnData objects directly.

Those consensus cell type annotations are now included in the merged SingleCellExperiment and AnnData objects available from the merge-sce module results, as part of the 2025-06-30 data release. In addition, we have addressed a bug in these merged objects which led to an incorrectly formatted cell_id column in the colData slot.

A full description how merged objects were prepared and their contents can be found in the ScPCA Portal documentation and in the merge-sce module in the OpenScPCA-nf repository.

To download merged objects for a given project, you can run the following command:

# Download merged objects for project SCPCP000001, for example
./download-results.py --modules merge-sce --project SCPCP000001

Note that the above command does require you to be logged into an AWS account with appropriate access privileges. Test data that does not require login is available by adding the --test-data flag.

For more details on options available in the download-results.py script, see the script documentation.