Description

The usage documentation (docs/usage.md) currently mirrors the code structure rather than guiding users to their use case. A reorganisation to be more user-centric would improve the experience.

Current structure

1. Pipeline parameters: see a different page
2. Samplesheet input
   1. Multiple runs of the same sample
   2. Linting
   3. Strandedness prediction
   4. Errors and reporting
   5. Full samplesheet
   6. BAM input
3. FASTQ sampling
4. Adapter trimming
5. Other pipeline steps...

Proposed structure

1. How to run the pipeline (example)
2. Samplesheet input
   1. Examples (simple, BAM input, etc.)
   2. Field definitions
3. How to configure specific features (e.g. prokaryotic mode, UMIs, GPU)
4. API-style organised reference docs
   1. Sequencing data quality assessment
   2. Sequencing data trimming
   3. Alignment to reference genome
   4. etc.

The goal is to guide users to their use case rather than presenting a wall of information.

Context

Raised by @adamrtalbot in the 3.23.0 release PR review.