update envs, tests and add argparse to margin_cons.py

[will-rowe]

This PR:

• tidies up the conda envs
  • removes pip installs from conda (artic-porechop now via conda)
  • consolidates medaka and nanopolish envs into a single env
  • adds muscle for upstream pipeline change
• now nanopolish 0.12.5 is in conda, update Travis to also test against OSX
• adds argparse to margin_cons.py so that the CLI can be tested easily
• updates README with a brief intro and some installation details
• adds command execution time to the minion log (as an additional tab-separated column)
• adds documentation for tests
• adds variant validation tests
• adds data download option for tests
• updates pipeline.py with some minor fixes:
  • removes duplicated guppyplex cmd
  • renames filter.py to filter_reads.py to avoid function overwrite
  • updated minion help text
• adds more documentation