Faster, more efficient version of the pipeline: many changes

The pipeline was restructured in different ways and a few bugs
were addressed.

- `hunter` is now split in more steps (this is why `viral_blast`
  and `summarise` have been added;
- `wolfpack` now runs by loading one contaminant in memory and
  mapping all samples against it, so that less time is spent
  loading and unloading from memory and decontamination is
  faster;
- blast is now called in parallel on mulitple cores, speeding
  up the viral database matching;
- blast uses its taxonomy database (setting environment variable
  BLASTDB);
- `extract_reads` has been corrected;
- `tax_orgs` now filters correctly on the coverage (bug).