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🛠️ Troubleshooting & Limitations

Current limitations

  • Do not change the structure of your input folder after running the pipeline. The first execution builds a config dataframe file (OUTPUT_DIRECTORY/config/config.tsv) that contains the list of cells and their associated paths. Changes to the folder structure will cause issues on subsequent runs.

  • Do not change the list of chromosomes between executions. For example, if you first run with chr17 only, do not run the next execution on all chromosomes in the same output directory.