Standardized workflow

 - directory structure follows snakemake workflow catalog's
   standardized usage more closely
 - configuration manual generated automatically from JSON schema
   see: config/config.html

For legacy V-pipe 1.x/2.x users:
 - the new directory structure requires adapting old INI files
   please refer to config/README.md section legacy-v-pipe-1xx2xx-users

NOTE:
 - 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.

Toward a new gen V-pipe

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')

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)

NOTE:
- 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.

Release of sars-cov2 branch in July 2020

Before rebasing to the latest master

Functionality to detect alignment bias

V-pipe 1 release

V-pipe 1.0 release candidate

V-pipe pre-release

Add parsing options and globals to a separate rule file

V-pipe SARS-CoV2 feature branch snapshot