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.