Commits on Oct 1, 2024

1. feat: CLIN-2947 Add optional exomiser process and tools parameter …

   This commit introduces the exomiser tool in the pipeline.
   Additionally, it introduces a new parameter called `tools`, which allows users to specify whether VEP, Exomiser, or both should be executed.
   
   Other changes:
   - Group vep output files (i.e. vcf + .tbi files) in subfolder `vep`.
   - Improve documentation (README, OUTPUT, USAGE, REFERENCE_DATA).
   - Refactor postprocessing workflow to use `def` for local variables and standardize variable names.
   - Update GitHub CI nf-test command: remove local tag constraint and activate CI mode.
   - Replace workflow diagram in README.

   

   DamienGnst authored and LysianeBouchard committed Oct 1, 2024
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