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.

[jbloom]

@ckikawa, can you just update this in the CHANGELOG too. As I understand it, this is just a bug fix so that can be a minor version (3.1.1) as no new functionality was added, it just makes something that already is supposed to happen work correctly.

Just briefly explain what is fixed and link to the issue, as in other CHANGELOG entries.

I don't quite understand @anloes's comment as I don't think anything needs to be added to README as this is just fixing a bug that prevented previously documented functionality from actually working correctly, right? Can you clarify that is correct with her?

[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.