FOI-Bioinformatics / nanometa_live

A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline functionality post-initialization.
GNU General Public License v3.0
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Enhanced Command-line Arguments and Config Update in `nanometa_new.py` #55

Closed druvus closed 1 year ago

druvus commented 1 year ago

Summary:

This PR extends the functionality of nanometa_new.py to include additional command-line arguments, enabling users to configure almost all settings in config.yaml directly from the command line.

Changes:

  1. Expanded CLI Arguments: Added multiple new command-line arguments that correspond to the settings in config.yaml.

  2. Config Update Mechanism: Extended the existing method to update config.yaml based on the newly introduced command-line arguments.

  3. Code Organization: Structured the code to segregate GUI and Workflow configuration updates.

  4. Type Checking: Included appropriate type definitions for the new arguments.