information about providing input to enclone (technical notes)

enclone only uses certain files, which are all in the outs subdirectory of a Cell Ranger pipeline
directory:

┌────────────────────────────────────────────────────────────────────────────┬──────────┐
│file                                                                        │  pipeline│
├────────────────────────────────────────────────────────────────────────────┼──────────┤
│all_contig_annotations.json                                                 │  VDJ     │
├────────────────────────────────────────────────────────────────────────────┼──────────┤
│vdj_reference/fasta/regions.fa                                              │  VDJ     │
├────────────────────────────────────────────────────────────────────────────┼──────────┤
│metrics_summary.csv                                                         │  GEX     │
├────────────────────────────────────────────────────────────────────────────┼──────────┤
│raw_feature_bc_matrix.h5                                                    │  GEX     │
├────────────────────────────────────────────────────────────────────────────┼──────────┤
│analysis/clustering/graphclust/clusters.csv                                 │  GEX     │
├────────────────────────────────────────────────────────────────────────────┼──────────┤
│analysis/pca/10_components/projection.csv                                   │  GEX     │
├────────────────────────────────────────────────────────────────────────────┼──────────┤
│per_feature_metrics.csv (optional, by default not generated by cellranger)  │  GEX     │
└────────────────────────────────────────────────────────────────────────────┴──────────┘

The first file is required, and the second should be supplied if Cell Ranger version 4.0 or
greater was used.  The others are required, in the indicated structure, if GEX or META/gex
arguments are provided.  The exact files that are used could be changed in the future.

Note that the VDJ outs directories must be from Cell Ranger version ≥ 3.1.  There is a workaround
for earlier versions (which you will be informed of if you try), but it is much slower and the
results may not be as good.

Note also that running "cellranger count" using only feature barcodes (antibodies),
             with less than ten features, will not yield all the needed files.  You can work
around this by adding "fake antibodies", to the feature list, so as to pad out the total number to
ten.