patch 1.2.0 > 1.2.1

[will-rowe]

This will close will-rowe/artic-tools#12 - where minion does not index the merged.vcf prior to checking for overlaps in --strict mode. I tracked this down to actually being a dependency change, as it worked in my old artic env (<1.2.0). The fix was just to add an extra VCF indexing command to minion.py if the pipeline was being run with --strict

This PR also:

• removes the reliance on a MultiQC artic module, instead we generate some stats from the align_trim output and the vcf_check output, storing these as a JSON file which MultiQC can munch on. I've included this as a feature enabled by --strict, so the extra files aren't produced using the existing pipeline.
• updates the doc with some missing minion sub commands
• bumps the version number with the patch

This branch will stay open after this PR is merged and I'll continue working toward the V1.3.0 release, where we want to increase the amount of info in the new report, bring in the new medaka version, and try out some additional stringency settings.

[kevinlibuit]

Curious to know if this will be made available as a versioned release?