Add `-h` flag to apps

[arisp99]

In an effort to improve docs, we should add the -h flag to all the MIPTools apps. Then the user can type the flag and get a nicely formatted man page. An example format that we could use is below:

Description

Usage:
singularity run [options] --app [app_options]

Options:
See 'singularity run'.

App Options:
-a Required. Description
-b Optional argument. Default value.
-h Print the help page.

Examples:
# Set paths
$ resource_dir=/bin/MIPTools/base_resources
$ dir=/work/usr/example

# Run app
$ singularity run
-B $resource_dir:/opt/resources -B $dir:/opt/analysis
--app -h