Add a preprocessing modules to the NextFlow pipeline

[St3451]

To streamline the workflow for users and enhance the usability of Oncodrive3D, it would be beneficial to include preprocessing modules that can handle the output of variant calling in VCF format. These modules could perform the following tasks:

• Compute Mutation Profile:
  Automatically generate the mutation profile required by Oncodrive3D to create a more accurate background model. This ensures that users don’t need to manually compute or format the mutation profile.

• Annotate Mutations Using VEP:
  Process the VCF file with Ensembl Variant Effect Predictor (VEP) to annotate mutations and prepare the input data in a format compatible with Oncodrive3D.

• Parse Mutations to MAF:
  Filter to map mutations to a single transcript for consistency (e.g., canonical ones) and parse the output to a MAF format.

Next steps:

• Update the Nextflow Pipeline:
  Integrate the preprocessing modules into the Nextflow pipeline, adding flags to enable or disable these steps as needed.