Improve reporting

[nictru]

Description of feature

Example reporting has already been implemented here. scFlow had really nice reports that should be used as inspiration (can be viewed here).

[nictru]

If you want to contribute here, adding plots of the UMAP representations of the integrations to the report would be a good starting point. UMAP creation currently happens in this module, more specifically in this script. After this line, the X_umap obsm field will contain the proper representation that can directly used for plotting.

Plotting itself should not be much of a problem. Make sure to use ${prefix}.png as the plot file name. In order to properly add the plots to the multiQC report, some additional steps are required:

1. Create a json file like it is done here
2. Change the output definition of the UMAP process so that the png and json are emitted properly (example)
3. Add a new channel to the CLUSTER subworkflow called ch_multiqc_files like here. Make sure to mix in the json outputs and emit the channel in the end of the CLUSTER subworkflow
4. Mix the subworkflow ch_multiqc_files into the global one like here
5. If necessary, adjust the multiQC config. General information on MultiQC can be found in the docs.

PS:
Because of the way the CLUSTER subworkflow is structured, you can be sure that the neighborhood graph that is used as a base for UMAP creation is based on the correct embeddings.