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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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Enhancements and Bug Fixes for Nanometa Live Pipeline #34

Closed druvus closed 11 months ago

druvus commented 11 months ago

Summary

This PR contains several important updates aimed at improving the Nanometa Live pipeline. The main focus is on enhancing compatibility with nested YAML configurations for species of interest, refining the BLAST database path, and minor improvements in file naming.

Details

  1. Nested YAML Compatibility:

    • The function create_validation_placeholders has been refactored to support the new nested YAML format for species_of_interest. This ensures compatibility and makes it easier to manage complex configurations.
    • Similar updates have been made to the function pathogen_update in nanometa_gui.py.

  2. BLAST Database Path Refinement:

    • The run_blast rule in the Snakefile has been updated to use the new subfolder data-files/blast for BLAST databases instead of blast_databases.

  3. File Naming Standardization:

    • In nanometa_prepare.py, file extensions have been standardized to .fasta for genomes.