notebooks/template_qc.qmd fails without 'alias' column in samplesheet.csv

[kieran-redpath]

create_diversity_plot() in notebooks/template_qc.qmd doesn't guard against a missing alias column at line 280 (also line 306), leading to this error message in nextflow.log if the alias column is missing and --alias_col is not defined:

ValueError: Value of 'hover_data_0' is not the name of a column in 'data_frame'.
Expected one of ['sample', 'shannon_entropy', 'inverse_simpson', 'gini_coefficient',
'hill_q0', 'hill_q1', 'hill_q2', 'patient', 'timepoint', 'origin', 'file']
but received: alias

I don't think this is intended behaviour, as tests/fixtures/valid_samplesheet.csv does not include the alias column, and other plotting functions in template_qc.qmd include a "if 'alias' in plot_df.columns" guard.

[RachelKarchin]

Hi Kieran-redpath

Thanks very much for your feedback.
TCRtoolkit is undergoing rapid development as it is now going to be a tool that handles both bulk and single cell TCR sequencing. As of today, we are making it private and it will be public once the new version is up and running.

Best