This is mainly a rewrite of the "USAGE.md" docs. It is now written to be a minimal but complete example run with both germline and somatic analysis. However, I think we should change it to be the best-practice commands later.

• Docs now have complete recommended commands for a complete analysis.
• The possible parameters are moved into a separate PARAMETERS.md.
• The parameters are divided based on the workflow script they apply to.
• The tsv documentation is renamed to INPUT.md which also includes the recommended directory structure when using the --sampleDir option.
• Customised profile is removed as we don't really explain how that would be done and it's not really intended for a regular user.

PR checklist

• PR is made against dev branch
• This comment contains a description of changes (with reason)
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated