The main configuration template & the step defaults should be checked for consistency and updated to reflect the new filesystems.

• main configuration: new locations for GRCh37/hs37d5 genome release & friends
• main configuration: add similar defaults for GRCh38 in comments (GRCh38.d1.vd1 used in somatic branch)
• main configuration: possibly add another GRCh38 flavor for germline usage
• main configuration: add feature annotation for expression, neo-epitope prediction, ...
• ngs_mapping: indices for bwa & bwa_mem2 tools, hs37d5, possibly GRCh38.d1.vd1
• somatic_variant_calling: default germline variants, panel of normals & common variants (GATK)
• somatic_variant_annotation: default VEP repositories
• many steps: exome panels