Release v1.3.0

• Refactor code around extracting read fractions and reads by taxa. This included removing support to extract sub-species and sub-sub-species reads to files because kraken assignments aren't confident enough to justify it. Also resolved a bug where the read counts in the summary file were on occasion double counted.
• Add kraken_confidence parameter
• Make alignment use short-read preset when we have illumina data
• Catch where out_dir or output used on command line instead of outdir
• Run extract steps with progressive memory allowed so that fewer resources required more often

What's Changed

• Paired run by @rmcolq in #66
• Fix missing read file 2 by @rmcolq in #70
• Dev refactor kraken by @rmcolq in #71
• Updated short read handling by @rmcolq in #68

Full Changelog: 1.2.1...1.3.0