Add site comparison of expected vs observed

[FerriolCalvet]

human generated summary

• Updated the computation of the site comparison so that it is a ratio of observed/expected more similar to dNdS.
• Use Poisson distribution to compute p-value of observing the observed given the expected as a mean.
• Fix bug and remove redundant code in annotation of panel filters
• Add the case of sitecomparison with using the mutated reads instead of individual mutations
• Update the columns defining VAF distortion

AI generated summary

This pull request includes significant changes to the omega configuration and workflow files to streamline the process and remove redundant steps. The most important changes include adding new configurations for SUBSETOMEGAMULTI, removing configurations related to omega_vaf_distorsioned, and updating the omega workflow to incorporate the new SUBSETOMEGAMULTI and SITECOMPARISONMULTI steps.

Configuration Changes:

• Added new configuration SUBSETOMEGAMULTI with specific filters and output format settings in conf/tools/omega.config.
• Removed configurations related to omega_vaf_distorsioned including PREPROCESSINGRED, ESTIMATORRED, SUBSETOMEGA_REDUCED, PREPROCESSINGEXP, ESTIMATOREXP, SUBSETOMEGA_EXPANDED, PREPROCESSINGOK, ESTIMATOROK, and SUBSETOMEGA_OK in conf/tools/omega.config.

Workflow Changes:

• Added SUBSETOMEGAMULTI and SITECOMPARISONMULTI modules to subworkflows/local/omega/main.nf. [1] [2]
• Updated the OMEGA_ANALYSIS workflow to include SUBSETOMEGAMULTI and SITECOMPARISONMULTI steps, ensuring they are properly integrated with existing steps. This includes joining SUBSETOMEGAMULTI output with ABSOLUTEMUTABILITIES and ABSOLUTEMUTABILITIESGLOBALLOC outputs and setting them for further comparison. [1] [2] [3]

[FerriolCalvet]

updates look good