Toward a new gen V-pipe

New features

This release incorporate numerous upgrades:

• Visualisation
• frameshift_deletions_checks
• sample consensus fasta generated by bcftools
• predicthaplo as an additional global haplotype engine
• support for extremely large cohorts
  (e.g., stats computed per-sample and merged, instead of all BAMs)
• snakemake resources
• Automatic testing
• Automatic Docker generation
• Snakemake standard JSON/YAML configuration
• virus_base_config instead of separate branches (like 'sars-cov2')

Legacy users

This is the last version that:

• uses a working directory structure that is still similar to…
• and can directly import configurations verbatim from…

…legacy versions of V-pipe 1.x/2.x and virus-branches (sars-cov2)

Working functionnality

• currently only the analysis of NGS viral data is fully tested and
  guaranteed stable.
• For other more advanced functionality (e.g., benchmarking) you might
  want to wait until a future release.