TRON-Bioinformatics/covigator-ngs-pipeline: Release v0.9.0

Changes Added a custom step phasing of clonal mutations. All clonal mutations (ie: clonal/not clonal determined by VAF) on the same amino acid are merged into a single mutation. This is not a read-backed phasing implementation which would allow to also phase intrahost mutations. Removed vt for decomposing complex mutations as the dependency was causing difficult to diagnose troubles in conda environments and it has virtually no impact in the output Improved documentatio