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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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Refactoring and Feature Enhancement for Improved Workflow Execution and Maintainability #35

Closed druvus closed 1 year ago

druvus commented 1 year ago

Summary:

This PR introduces refactoring and feature improvements to the nanometa_live project, specifically the Snakefile and nanometa_backend.py.

Changes:

  1. Refactored Directory and File Checking in Snakefile:

    • Moved the logic that waits for the directory and files to exist into a reusable function, wait_until_condition_met.
    • This change makes the code more modular and easier to understand.

  2. Improved Execution of Snakemake Workflow:

    • Modified the execute_snakemake function in nanometa_backend.py to accept an additional parameter for specifying the config file path.
    • This ensures that the correct config file is used when executing the Snakemake workflow.

Why is this change necessary?