Rework 3-dir format into 4-dir to track library preps as well; includes some additional parsers and database access changes
Record project-level workflow PIDs with shelve
Outline future work. I should write some tests.
Return subprocess.Popen objects from piper_ngi instead of PIDs; remove cruft; rework workflow concept from e.g. dna_alignonly to e.g. NGI
Finish implementing the local tracking of processes and implement synchronization with Charon