Closed mkeays closed 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.
CODEX datasets will include a CSV file called
channelNamesReport.csv
which will contain a list of the channel names andTrue
orFalse
to denote whether the antibody passed (True
) or failed (False
) laboratory QC. Failing antibodies should not be included in theextract/expressions
TIFF (and OME-TIFF) files.bin/create_cytokit_config.py
and not adding failed channel names to theoperator: extract: expressions
section of the Cytokit YAML config.channelNamesReport.csv
file needs to be picked up bybin/collect_dataset_info.py
.