Update usage.rst

[Leo-GG]

Corrected typo hiding the command to run the whole pipeline. Added additional notes about assembly, mapping, classify and annotate rules.

• I have run pytest .tests/ on a local deployment and the tests passed successfully
• If this adds a new output file, I have added a check to .tests/targets.txt
• If this fixes a bug, I have added or modified an appropriate test
• If this adds or modifies a rule that uses FASTQ files, the input accepts gzipped FASTQ and outputs gzipped FASTQ, or marks uncompressed FASTQ output as temp

If this is for a release:

• I have updated documentation
• I have updated the hardcoded version at the top of install.sh to match what this release's version will be
• I have created a release archive that will be attached to this release (bash dev_scripts/generate_archive.sh)

[Ulthran]

Thanks for the contribution @Leo-GG! Looks like something has broken either in snakemake or in one of our container images... I'll have to do some investigating to see what that is. Not something in your PR, this would've been picked up by the next scheduled test run.