Reorganise arguments for clearer syntax

Changes:
 - Grouped arguments into sections based on _what they do_
 - Reordered slightly to go in chronological order of the pipeline and set up
 - I think it's clearer for a new user

Fixes nf-core#1090

CHANGELOG.md

@@ -23,6 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
 - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
 - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
+- [PR ####](https://github.com/nf-core/rnaseq/pull/####) - Reorganise command line for better usability
 
 ## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02