Aquamis qc

[omegatro]

• Added aquamis-based quality reporting.
• Checks species-specific thresholds, if available, then genus-specific thresholds, if available.
• In all cases checks species-agnostic thresholds.
• Currently checks the following merics:
  • 'GC (%)',
  • 'N50',
  • 'Total length',
  • '# contigs (>= 0 bp)',
  • '# contigs (>= 1000 bp)'
  • 'assembly_coverageDepth',
  • 'contig_hit1_species_fraction',
  • 'q30_rate_after'
• Provides value of each parameter, reference range, QC-status and color code.
• Also includes species, sample id, analysis batch, and timestamp of the last update for AQUAMIS thresholds
• Solution for #26