Pipeline update / Manual template merge

[ewels]

• Manually merged the three new template updates and fixed all merge conflicts.
• Moved all parameter documentation into new nextflow_schema.json file.
• Renamed --reads to --input to match new nf-core guidelines.
• Updated CamelCase and Upper Case parameters to be lower_case_snake_case
• Changed dev version from 1.0.1 to 1.1 as now has fairly major changes.

PR checklist

• This comment contains a description of changes (with reason)
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

[ewels]

Merging this PR should auto-merge / close #51 without needing any additional actions.

[ewels]

Ok, I think that this PR is good to go now 🚀

Tests should all be passing, no additional content to update before merge that I'm aware of ✅

Just need a 👍🏻 review and merge.