pre- and post- filtering metadata capture

[ergonyc]

In 'merge_and_plot_qc.py' dump the metadata to something like "initial_metadata.csv"

move post- metadata dump from 'annotate_cells.py' to 'add_harmony.py'

implications:

• [ ] output_metadat_file arguments need to be removed from 'annotate_cells.py' and csv dump removed
• [ ] output_metadat_file arguments need to be added to 'add_harmony.py' and csv dump added
  • note: UMAP_1 and UMAP_2 to be added before dump (but not duplaced in adata.obs)
• [ ] output_metadat_file arguments need to be added to 'merge_and_plot_qc.py' and csv dump added
• [ ] wdl calls to "merge_and_plot_qc.py" and "add_harmony.py" need to include "--output-metadata-file" args

[ergonyc]

full path to scripts in docker/scvi/scripts/