feat: add virema

[gp201]

This pull request introduces several significant updates to the pipeline, including the addition of new modules and workflows, improvements to existing processes, and code standardization. Below is a summary of the most important changes grouped by theme:

New Modules and Workflows

• Added VIREMA module: Includes a new VIREMA process for viral recombination analysis, along with its corresponding environment.yml file. This process outputs BED, BAM, and SAM files, as well as coverage statistics. (modules/local/virema/main.nf, modules/local/virema/environment.yml) [1] [2]
• Added GROUP_FASTA module: Introduced a new process to group FASTA files based on metadata. (modules/local/group_fasta/main.nf)
• Added DVG workflow: Implements a workflow for detecting defective viral genomes, integrating the VIREMA process and other modules. (subworkflows/local/dvg/main.nf)
• Added COMBINE_SAMPLE_CONSENSUS workflow: Combines sample consensus sequences into grouped FASTA files using the GROUP_FASTA module. (subworkflows/local/utils_nfcore_flusra_pipeline/main.nf)

Enhancements to Existing Workflows

• Updated PROCESS_SRA workflow: Integrated the DVG and COMBINE_SAMPLE_CONSENSUS workflows, replacing direct consensus handling with a more modular approach. (subworkflows/local/process_sra/main.nf) [1] [2] [3]
• Improved MILK_FREYJA workflow: Fixed a trailing comma in parameter handling. (subworkflows/local/milk_freyja/main.nf)

Code Standardization

• Consistent variable interpolation: Replaced $variable with ${variable} across multiple modules for improved readability and consistency. (modules/nf-core/bwa/mem/main.nf, modules/nf-core/fastp/main.nf, modules/nf-core/freyja/demix/main.nf, modules/nf-core/ivar/variants/main.nf, etc.) [1] [2] [3] [4] [5]
• Added braces to conditional blocks: Improved code clarity by enclosing all conditional blocks in braces. (modules/nf-core/fastp/main.nf) [1] [2]

These changes collectively enhance the pipeline's modularity, maintainability, and functionality.