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naobservatory / mgs-pipeline

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Added kraken assignment to creation of hvreads. #29

Closed simonleandergrimm closed 8 months ago

simonleandergrimm commented 8 months ago

@jeffkaufman, as discussed, I slightly edited the run.py code to add Kraken assignment information to *.hvreads.json.

jeffkaufman commented 8 months ago

Thanks! This looks correct, but there are other things we'll need to do after this.

  1. Right now run.py file has:

    existing_outputs = get_files(args, "hvreads",
                            # date we added quality scores
                            min_date='2023-09-18')

    which will need to be updated to the current date so old hvreads are regenerated.

  2. Everyone will need to rm -r dashboard/hvreads/

  3. Everything downstream that reads hvreads will need to be updated to use the new format. I think the easiest way to do this is just make the change and then fix what crashes.