Genome-grist

What's Changed

* [MRG] update ignore_ident code for later use too by ctb in https://github.com/dib-lab/genome-grist/pull/259

**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.9.2...v0.9.3

What's Changed

* [MRG] add code to support skipping genomes by ident by ctb in https://github.com/dib-lab/genome-grist/pull/255
* [MRG] update snakemake version in `environment.yml`, & other minor fixes by ctb in https://github.com/dib-lab/genome-grist/pull/253
* [MRG] add gh-pages deploy action by ctb in https://github.com/dib-lab/genome-grist/pull/252
* [MRG] add pip check to GitHub actions by ctb in https://github.com/dib-lab/genome-grist/pull/254
* [MRG] update github actions to use modern conda/caching by ctb in https://github.com/dib-lab/genome-grist/pull/256
* [MRG] update actions to make sure right version(s) are being used by ctb in https://github.com/dib-lab/genome-grist/pull/258



**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.9.1...v0.9.2

What's Changed

* [MRG] update sourmash and screed versions by ctb in https://github.com/dib-lab/genome-grist/pull/251
* [MRG] add dependabot by ctb in https://github.com/dib-lab/genome-grist/pull/243
* Bump actions/setup-python from 1 to 4 by dependabot in https://github.com/dib-lab/genome-grist/pull/244
* Bump actions/checkout from 2 to 3 by dependabot in https://github.com/dib-lab/genome-grist/pull/245
* Update pytest requirement from ~=5.1.2 to >=5.1.2,<7.3.0 by dependabot in https://github.com/dib-lab/genome-grist/pull/247
* Update click requirement from <8,>=7 to >=7,<9 by dependabot in https://github.com/dib-lab/genome-grist/pull/248
* Bump lxml from 4.6.4 to 4.9.1 by dependabot in https://github.com/dib-lab/genome-grist/pull/249
* [MRG] update snakemake and sourmash versions by ctb in https://github.com/dib-lab/genome-grist/pull/242
* [MRG] run actions regularly by ctb in https://github.com/dib-lab/genome-grist/pull/250


New Contributors
* dependabot made their first contribution in https://github.com/dib-lab/genome-grist/pull/244

**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.9.0...v0.9.1

There are several significant changes to output files from v0.8.4 that will affect downstream processing. Upgrading may also require rerunning existing analyses because filenames have changed. Please see [genome-grist225](https://github.com/dib-lab/genome-grist/issues/225) for a summary guide to upgrading to v0.9.0 from v0.8.4.

Details

Significant new features:
* remove abundance trimming from the default genome-grist workflow (199)
* change column names in mapping summary files; add count of mapped reads. (209, 219)

Other changes::

* fix calculation of memory required for prefetch step (229)
* fix trim-low-abund ksize to match sourmash db ksize (218)
* Allow everything _but_ hyphens and periods in sample names (188)
* switch to gzipped sourmash input/output files (213)
* add an initial summary of output files and their contents (211)
* fix notebook to properly handle a single mapping result (214)
* Speed up `copy_local_genomes.py` with symbolic links (181)
* fix returncode (200)
* provide a better error message for empty prefetch; upgrade sourmash versions (195)
* fix genome download rule (233)

**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.8.4...v0.9.0

What's Changed

* [MRG] update notebooks for long contig names; add normalized snp figure (fig 11) by ctb in https://github.com/dib-lab/genome-grist/pull/171
* [MRG] fix the ksize/moltype specified for `sourmash gather` by ctb in https://github.com/dib-lab/genome-grist/pull/173
* [MRG] switch to using .sig.zip signatures; add `summarize` target by ctb in https://github.com/dib-lab/genome-grist/pull/175
* [MRG] fix local genomes config file in docs by mr-eyes in https://github.com/dib-lab/genome-grist/pull/182

**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.8.3...v0.8.4

What's Changed

* [MRG] add VCF-calculating code from 124 by ctb in https://github.com/dib-lab/genome-grist/pull/165
* [MRG] fix and adjust gather-based known/unknown reporting by ctb in https://github.com/dib-lab/genome-grist/pull/166
* [MRG] update mapping notebook to include SNP graph, and etc. by ctb in https://github.com/dib-lab/genome-grist/pull/168

**Full Changelog**: https://github.com/dib-lab/genome-grist/compare/v0.8.2...v0.8.3