Add Preset Parameters for Common Analyses in BACPAQ Workflow

[anwarMZ]

Description of feature

The BACPAQ workflow currently requires users to specify parameters for each analysis step, which can be challenging for non-bioinformatics experts who may not be familiar with the best practices for each type of analysis. This task proposes adding preset parameters for common analyses, such as quality control (QC), taxonomy analysis, and various genome annotation steps. These presets would offer an accessible, “ready-to-go” configuration that minimizes the need for in-depth bioinformatics knowledge and helps users get consistent, reliable results.
1. Provide a user-friendly experience by giving non-experts a reliable starting point.
2. Improve reproducibility by standardizing parameters across common analysis types.
3. Save time for users who might otherwise need to research or experiment with settings for each new analysis.

The following tasks are required to close this issue:

• Identify common analysis types (such as QC, taxonomical analysis, antimicrobial resistance gene prediction, variant detection, etc) & create preset parameter files
• Identify additional genomic analysis scenarios; brainstorm more genomic analysis scenarios that BACPAQ users may encounter where presets would be helpful. Prioritize the scenarios based on user needs and workflow feasibility, considering whether additional presets would enhance BACPAQ’s versatility and usability.
• Update documentation: Write detailed documentation for each preset, explaining each configuration, when to use it, and what results users can expect. Provide examples and scenarios to help users understand how to choose and apply presets effectively.
• Testing and Validation of Presets: Conduct testing to validate each preset parameter file in real analysis scenarios.