Version 3 of the format

[LTLA]

• Add CRISPR QC, normalization, PCA.
• Rename RNA steps to have a rna_* prefix.
• Reorganize input files for easier parsing.
• Store session information somewhere.
• Remove skip from the QC parameters.
• Save the use_* parameters for cell_filtering.
• Rejig the weights for combine_embeddings.
• Marker detection should skip AUCs, add LFC
• SNN Graph detection should add extra parameters