[BUG] missing rad files?

[jashapiro]

Describe the bug
Alevin-fry quant can't find rad files.

To reproduce

This bug occurred with an external user, who had the following output:

Error executing process > 'map_quant_rna:fry_quant_rna (X_7316-1663_5pr_150PE-rna)'

Caused by:
  Process `map_quant_rna:fry_quant_rna (X_7316-1663_5pr_150PE-rna)` terminated with an error exit status (101)

Command executed:

  alevin-fry generate-permit-list       -i X_7316-1663_5pr_150PE-rna       --expected-ori rc       -o X_7316-1663_5pr_150PE-rna       --unfiltered-pl 737K-august-2016.txt
  
  alevin-fry collate       --input-dir X_7316-1663_5pr_150PE-rna       --rad-dir X_7316-1663_5pr_150PE-rna       -t 8
  
  alevin-fry quant       --input-dir X_7316-1663_5pr_150PE-rna       --tg-map Homo_sapiens.GRCh38.104.spliced_intron.tx2gene_3col.tsv       --resolution cr-like-em       -o X_7316-1663_5pr_150PE-rna       --use-mtx       -t 8 
  # remove large files
  rm X_7316-1663_5pr_150PE-rna/*.rad X_7316-1663_5pr_150PE-rna/*.bin

Command exit status:
  101

Command output:
  (empty)

Command error:
  2022-09-09 11:27:34 INFO number of unfiltered bcs read = 737,280
  thread 'main' panicked at 'could not open input rad file: Os { code: 2, kind: NotFound, message: "No such file or directory" }', src/cellfilter.rs:609:52
  note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Expected behavior
The step should have run...

Additional context
Attaching a the command.run file that seems to contain the error:
command.run.txt

We would not expect the file to be deleted, but it is possible that tracing the symlinks is causing trouble. If we can force copying of the input files at this stage (or the output of the previous stage) that might be a solution worth trying.