feat: unit test and refactoring

[nakib103]

NW-55

Unit test and CI

• added for all modules, subworkflows, workflows and functions.
• CI for linting and building Rust binaries and python ensembl-variation-utils package.

ensembl-variation-utils package

The nextflow bin were taking a lot responsibility of figuring out the file locations, talking with databases etc. These responsibility has been taken of and given to a separate python package called ensembl-varation-utils. It has 3 separate modules -

• clients: to establish connection and talking with clients. We currently have DB clients that talks to metadata and core databases but it can be replaced in future with gRPC or REST.
• file_locator: this module knows the internal /nfs and external ftp directory and file structure and can discover files such as FASTA, GFF, VEP cache etc. and do file operations.
• vep_config: similar to file_locator but specialised for VEP plugin and custom annotation data files.

VEP config generation

Instead of hardcoding everything to generate_vep_config.py script now we accept a JSON config which can be fashioned for each run with greater degree of variability. See assets/example for an example of a json config.

[mluypaert]

Please rebase this to merge into main, and resolve any merge conflicts arising so the PR can be merged upon approval and only need approving once (as the merge conflict resolutions can result in review needing to be repeated).