Genome-grist

What's Changed

* [MRG] split identifiers on whitespace, not just spaces. by ctb in https://github.com/dib-lab/genome-grist/pull/150
* [MRG] minor updates, incl. sourmash version updates. by ctb in https://github.com/dib-lab/genome-grist/pull/160
* [MRG] compress output signatures by ctb in https://github.com/dib-lab/genome-grist/pull/158
* [MRG] print out unknown config variables by ctb in https://github.com/dib-lab/genome-grist/pull/161
* [MRG] add a flag to prevent metagenome download from SRA by ctb in https://github.com/dib-lab/genome-grist/pull/157
* [MRG] add sourmash_database_threshold_bp to docs & config check by ctb in https://github.com/dib-lab/genome-grist/pull/162


**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.8.1...v0.8.2

What's Changed

* [MRG] fix identifier munging for local databases by ctb in https://github.com/dib-lab/genome-grist/pull/145

**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.8.0...v0.8.1

Significant documentation updates as well as configuration file updates to support local databases.

What's Changed

* [MRG] Fix `download_matching_genomes` target by ctb in https://github.com/dib-lab/genome-grist/pull/125
* [MRG] extract the depth summary code from the Snakefile to a script by ctb in https://github.com/dib-lab/genome-grist/pull/128
* [MRG] several minor updates and cleanup by ctb in https://github.com/dib-lab/genome-grist/pull/129
* [MRG] support local genome collections (including private genomes) by ctb in https://github.com/dib-lab/genome-grist/pull/130


**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.7.4...v0.8.0

Developer fixes:
* updated lxml (== 4.6.4) and python versions (>= 3.7, < 3.10)

Minor new features:
* add taxonomy output via `sourmash tax` on the gather results (100)
* add a gather-only summary step (99)
* update to use sourmash picklists and manifests for significant decrease in disk space, increase in speed (94, 103)
* make missing config options clearer (102)
* add CLI usage info (90)
* re-try logscale and gridlines to new figure 10 (87)
* add per-genome coverage & abundance reporting (85)

Developer fixes:
* add sourmash to the papermill environment (111)
* Update Snakemake version (106)
* update dependencies in setup.py and environment.yml (89)

Documentation updates:
* change default targets and update help docs (101)
* fix README for new targets (109)

Update to sourmash 4.1.1, downgrade sra-tools, use lower-memory signature outputs, and output a prefetch CSV (https://github.com/dib-lab/genome-grist/pull/83).