Accommodate Mbovis reference

[abhi18av]

This PR introduces changes related to adapting MAGMA pipeline for the Mbovis related analysis.

This pull request primarily removes the custom bwa/mem module from the codebase, including its process definition, environment, metadata, and tests. It also updates container configuration for SNPEFF, adjusts a reference genome in SNPEFF arguments, and improves parameterization in some local modules. Additionally, it cleans up the modules.json file by removing several module entries.

The most important changes are:

Module Removal and Cleanup

• Removed the entire custom bwa/mem module, including its process definition (main.nf), environment file (environment.yml), metadata (meta.yml), and all associated tests (tests/main.nf.test). [1] [2] [3] [4]
• Cleaned up modules.json by removing references to many modules, including bwa/mem, and others such as bcftools/merge, samtools/index, and more.

Container and Configuration Updates

• Updated conf/docker.config to assign a dedicated container image for SNPEFF processes, separating it from the general container used for other tools.
• Changed the SNPEFF arguments in default_params.config to use the Mycobacterium_bovis_gca_000729755 reference instead of Mycobacterium_tuberculosis_h37rv.

Parameterization Improvements

• Updated hardcoded reference names in modules/local/tbprofiler/vcf_profile__cohort.nf and modules/local/tbprofiler/vcf_profile__lofreq.nf to use the params.ref_fasta_basename parameter for better flexibility. [1] [2]