specify counts columns in manual_drops

[ckikawa]

This pull request should resolve #45 by adding additional elif statements to a cell of process_plate.ipynb where manual_drops are removed from the counts dataframe. I tested this with multiple wells on some recent H3N2 ngs-neut data.

As is, single wells/barcodes cannot be specified in lists (as indicated in README). They must be added as individual lines with dashes. If this is expected behavior, ignore this comment. Otherwise, I can add this detail to README?

[anloes]

I think we should add instructions to the README.md, if was not immediately obvious that this is what should be done, an example would work.

[anloes]

Yes, you are correct that this was a bug fix. However, there is not currently an example of how a single well or a barcode should be listed for exclusion. It was unclear if they should be in brackets around the entry or if these could just be listed as strings. I would recommend we update the README.md section on manual drops to show an example of each, i.e.:

manual_drops: barcode_serum_replicates:

• [AGTCCTATCCTCAAAT, M099d0] wells:
• A1

[jbloom]

It should just be a list, which can be specified in either of two ways in YAML:

wells: [A1, A2]

or

wells:
  - A1
  - A2

It says this verbally in README, but you can add in example if you want @ckikawa

[ckikawa]

@jbloom, I see. I think this was just a YAML formatting quirk that I wasn't familiar with. I was trying (and failing) with:

wells:
  - [A1, A2]

I've updated the CHANGELOG but I'm not sure an example in README is necessary.