Add rerun triggers to run sub command

[skchronicles]

Add --rerun-trigger to run sub command

This adds a mechanism to control how snakemake decides what rules to re-run. By default, this option is set to the following: ['mtime', 'params', 'input', 'software-env', 'code'] which can cause upstream rules to re-run unexpectedly.

Add something to the docs stating if this occurs, then this should be set to --rerun-trigger mtime. This allows for the user to decide how/why rules are re-run.