Merge branch 'dev'

Fix FASTA shuffling

Fix(nanosim): correct SAM POS, CIGAR generation, and ID parsing

Fix NanoSim3 CIGAR strings and unmapped read filtering

Calculate safe max read length for nanosim

Add optional external config and pipeline-specific includes

Merge branch 'dev-get-genomes-update' into dev

Set cpus=1 and quote in process get_genomes

Merge pull request #234 from CAMI-challenge/codex/update-nanosim-to-use-coverage-parameter

Enable multithreading for Nanosim simulation

Update genome-to-OTU assignment algorithm

Fix genome-to-OTU assignment (part 2)

Fix genome-to-OTU assignment

Add ncbi_taxdump_file & max_rank parameters for get_genomes.py, update packages

Fix boolean parameter parsing in get_genomes.py