hubmapconsortium / codex-pipeline

CODEX data processing code
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Handle channel names report CSV files #11

Closed mkeays closed 4 years ago

mkeays commented 4 years ago

CODEX datasets will include a CSV file called channelNamesReport.csv which will contain a list of the channel names and True or False to denote whether the antibody passed (True) or failed (False) laboratory QC. Failing antibodies should not be included in the extract/expressions TIFF (and OME-TIFF) files.

mkeays commented 4 years ago

This is not needed before the first release. The CSV files will probably be present but there is insufficient time to re-run all the pipelines to apply these code changes. This is fine -- users will be able to see that it is known which antibodies failed QC, if they encounter blank channels.