Update plate 6 samples

[jenna-tomkinson]

Update Plate 6

In this PR, samples parameter was updated for both normalize and feature select for Plate 6 to select samples from the iNFixion cell line and WT and Null genotypes.

Should we also update this for the traditional bulk method?

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[gwaybio]

An important question! Also, what is the feature selected dataframe shape? (it would be helpful to know how many features were removed)

[jenna-tomkinson]

@gwaybio I have updated the environments to account for the bug fix. Plate 6 single cells have now been processed correctly with the samples parameter.

I did add two small changes to this PR that you can address:

1. Small refactor to regular expression in CP pipeline to correctly extract plate metadata, which is the first part to solve issue Update metadata regular expression in analysis.cppipe files #57. I will need to rerun Plate_6 with CP to properly extract the plate metadata later.
2. I noticed the traditional bulk pipeline did not remove the contaminated HET cells or use samples parameter, so I updated it and reprocessed plates 3, 3 prime, 4, 5, and 6 just to be accurate. Depending on manuscript, we might not need these but I wanted to make sure it was accurate.

NOTE: Due to trying to install the correct version of pycytominer in my main environment (held pycytominer, cytotable, and cellprofiler), it was unfortunately a mistake as the environment broke and can no longer be used (of course cause cellprofiler). I had to delete the environment and reinstall, just so CellProfiler could work. Depending on your opinion, we could reprocess all of the plates with the new environment, but that might not be necessary.