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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Improvment in nanometa-new and addition of nanometa-prepare #27
This PR introduces enhancements to nanometa-new and adds a new utility called nanometa-prepare.
Changes in nanometa-new
Dynamic Config Update: Added a feature that allows config.yaml to be dynamically updated during the nanometa-new process from the command-line arguments.
YAML Parsing Library Switch: Moved from PyYAML to ruamel.yaml for advanced comment handling in YAML files.
Introduction of nanometa-prepare
nanometa-prepare aims to streamline the process of setting up the genomic databases. It automates several tasks:
Species Lookup: Utilizes GTDB API calls for species name resolution.
Kraken2 Database Parsing: Incorporates the kraken2 inspect tool for database information retrieval.
Genome Downloads: Automatically downloads the necessary genomes.
BLAST Database Building: Automates the process of building BLAST databases from the downloaded genomes.
Motivation
The dynamic update of config.yaml enables more flexible pipeline setups.
Switching to ruamel.yaml allows the preservation and better handling of comments, which enhances configuration file maintainability.
nanometa-prepare aims to automate tedious tasks, making it easier for users to set up their genomic databases.
Summary
This PR introduces enhancements to
nanometa-newand adds a new utility callednanometa-prepare.Changes in
nanometa-newconfig.yamlto be dynamically updated during thenanometa-newprocess from the command-line arguments.Introduction of
nanometa-preparenanometa-prepareaims to streamline the process of setting up the genomic databases. It automates several tasks:kraken2 inspecttool for database information retrieval.Motivation
config.yamlenables more flexible pipeline setups.nanometa-prepareaims to automate tedious tasks, making it easier for users to set up their genomic databases.