Tracking: input/output

[nathanin]

For a command-line interface we want a preprocess command like:

$ codex preprocess /raw/data --name sample --region 1 -o /output/dir

Should create /output/dir and

• [ ] place preprocessed images under /output/dir/images
• [ ] make a record of arguments, intermediate files/settings at /output/dir/settings.txt
• [ ] QC metrics under /output/dir/qc