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dms-vep / flu_h3_hk19_dms

Analysis of a multi-mutant, barcoded influenza H3 library in the A/HongKong/45/2019 background.
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add data from Perth2009 DMS by Juhye Lee and Rachel Eguia #36

Closed jbloom closed 1 year ago

jbloom commented 1 year ago

@fwelsh, this pull request adds a CSV with the data from Perth/2009 DMS for relevant samples. This CSV is tracked. The notebook will be rendered as part of the docs when you run the entire pipeline with this added, although I have not done that and will leave it to you.

Note that if you wanted you could include a lot of your scratch_notebooks as custom rules in the pipeline as I have done here if you want to have them integrated rater than separate manual steps, although up to you whatever you prefer.

fwelsh commented 1 year ago

Great, thank you! I'll run this and see how it looks. Most of the scratch_notebooks are one-off analyses, but there are a few I can clean up and integrate into the pipeline.

fwelsh commented 1 year ago

@jbloom since adding these custom rules, the pipeline now fails with Error in rule docs_index: and the specific error should be in results/logs/docs_index.txt but that file is empty. The Perth09 data does seem to process correctly: I have a folder in results/ now containing eguia_avg_sel_tidy.csv, lee_avg_sel_tidy.csv, and merged_escape.csv, plus notebooks/process_perth2009_data.ipynb. This notebook and results/perth2009/merged_escape.csv are listed as docs_index inputs. I'm not sure how to troubleshoot this without an actual error message, do you know what's going on?