Change Nanopore defaults

[mbhall88]

Changed

• Nanopore preset --ont defaults to an expected error rate of 0.08 and ploidy
  'haploid' [closes ONT flag default settings #134]
• Default Illumina expected error rate change from 0.05 to 0.001 [closes Default error rate for Illumina #133]. If you don't want to make this change I can easily revert this.

Note: this branch is based off the tip of #138, so once that PR is merged, this PR will be simplified down to the last 2 commits.

[martinghunt]

I vote definitely change all the nanopore defaults.

I'd prefer to rerun the mykrobe paper data before changing any illumina defaults.

[mbhall88]

I vote definitely change all the nanopore defaults.

I'd prefer to rerun the mykrobe paper data before changing any illumina defaults.

Ok, I have changed the Illumina error rate back to 0.05.

It seems strange though given this

mykrobe/src/mykrobe/cmds/amr.py

Lines 340 to 342 in b4a19c2

	if args.guess_sequence_method and kmer_count_error_rate > 0.001:
	logger.warning("Guess sequence method is on, and we've guessed ONT")
	args.ont = True

we seem to acknowledge that anything with an error rate over 0.001 is not Illumina, but set the expected error rate for Illumina to 0.05...