Contents are stored inside an inputs HDF5 group at the root of the file.
The cell_labelling group itself contains the parameters and results subgroups.
Definitions:
rna_available: whether RNA data is available in the dataset. This is typically determined from theinputsstep.num_clusters: number of clusters generated in the analysis. This is determined by thechoose_clusteringstep.
parameters should contain:
human_references: a string dataset defining the human reference datasets used for labelling. Each entry contains the name of a reference dataset, e.g.,"BlueprintEncode".mouse_references: a string dataset defining the mouse reference datasets used for labelling. Each entry contains the name of a reference dataset, e.g.,"ImmGen".
If rna_available = false, results should be empty.
Otherwise, results should contain:
per_reference: a group containing the label assignments for each cluster in each reference. Each child is named after its corresponding reference as listed inparameters, though not all references listed inparametersneed to be present here. Each child is a 1-dimensional string dataset of length equal tonum_clusters, where each entry contains the assigned label for the corresponding cluster.
For multiple references of the relevant species, results will also contain:
integrated: a string dataset of length equal tonum_clusters. This specifies the reference with the top-scoring label for each cluster, after integrating the results of all per-reference classifications.
Updated in version 3.0, with the following changes from the previous version:
- Cell labelling results are now optional if RNA data is not available.