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hubmapconsortium / portal-containers

Docker containers to pre-process data for visualization in the portal
MIT License
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Fix cluster name handling in atac-seq script #118

Closed keller-mark closed 1 year ago

keller-mark commented 1 year ago

More info on slack: https://hubmapconsortium.slack.com/archives/C02NA0BJW2C/p1677856738129809

Traceback (most recent call last):
  File "/main.py", line 110, in <module>
    main(args.input_dir, args.output_dir)
  File "/main.py", line 89, in main
    cell_sets_json=arrow_path.with_suffix('.cell-sets.json'),
  File "/main.py", line 39, in arrow_to_json
    for (k,v) in df_items
  File "/main.py", line 39, in <dictcomp>
    for (k,v) in df_items
ValueError: invalid literal for int() with base 10: 'C1'

Upstream changes violated the assumption that cluster names are always integers