Small fixes to sample QC notebook #773
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scripts/notebooks/SampleQC.ipynb
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| "sample_set_tbl = sample_set_tbl[sample_set_tbl['entity:sample_set_id'].str.contains('KJ_EvidenceQC_Updates')]" | ||
| "sample_set_tbl = sample_set_tbl[sample_set_tbl['entity:sample_set_id'].str.contains('KJ_EvidenceQC_Updates')]\n", | ||
| "file_path = generate_file_path(TLD_PATH, 'artifacts', 'sample_sets_qc.tsv')\n", | ||
| "save_df(WS_BUCKET, file_path, sample_set_tbl)" |
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Can we comment out the reference to KJ_EvidenceQC_Updates? I see it's used as an example, but probably should be commented out. And maybe even change the substring being searched for to something more generalizable rather than 'KJ'.
This must've been missed in the first pass.
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Maybe you can add 1-2 new lines between the comment to optionally filter to only include a subset of batches. and the two lines that now follow it (generate_file_path and save_df)?
I worry that folks will simply ignore a single-line comment. Alternatively, we can add a green box for (optional) user input to make this more clear, but believe we decided against this in previous iterations.
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Could add a green box and a new variable SUBSTRING and only run the following lines if SUBSTRING is not None?
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Looks great now, thanks! |
Updates include:
Testing:
Tested in clone of public workspace on reference panel data, with and without reference PED file. Cleared outputs and tested re-upload