Genome-grist

Many significant improvements to internals; no major new features.

* use `fasterq-dump` instead of `fastq-dump` to enable multithreaded downloads (75)
* use`sourmash prefetch` from sourmash v4.1.0 (68)
* use scratch instead of tmp (76)
* use fastp instead of trimmomatic (72)
* use temp directory so snakemake automatically deletes temp files (71)
* add mamba to environment yml; update sourmash to 4.x (74)
* update sourmash and screed versions; turn on python -Werror (67)

New features

* Add more reporting for output read/kmer stats (56); add tests for new reporting (65)

Fixes, updates, and refactors

* Fix abundance calculations (64)
* GitHub actions update; sync with screed setup (58)
* Change ftp to https for genome downloads (57)
* Adjust memory requirements; update README with quickstart tutorial, memory requirements and other text (54)

Fix issues for a non-developer install.

Provide an end-to-end workflow with checkpoints; many minor improvements.

Much cleaning, more good. Testing, also good.

Add prefetching of containment matches to speed up gather (16)
Add tests and github actions for CI (19)