v0.9.3

What's Changed

• [MRG] update ignore_ident code for later use too by @ctb in #259

Full Changelog: v0.9.2...v0.9.3

v0.9.2

What's Changed

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

Full Changelog: v0.9.1...v0.9.2

v0.9.1

What's Changed

• [MRG] update sourmash and screed versions by @ctb in #251
• [MRG] add dependabot by @ctb in #243
• Bump actions/setup-python from 1 to 4 by @dependabot in #244
• Bump actions/checkout from 2 to 3 by @dependabot in #245
• Update pytest requirement from ~=5.1.2 to >=5.1.2,<7.3.0 by @dependabot in #247
• Update click requirement from <8,>=7 to >=7,<9 by @dependabot in #248
• Bump lxml from 4.6.4 to 4.9.1 by @dependabot in #249
• [MRG] update snakemake and sourmash versions by @ctb in #242
• [MRG] run actions regularly by @ctb in #250

New Contributors

• @dependabot made their first contribution in #244

Full Changelog: v0.9.0...v0.9.1

v0.9.0

Upgrading to v0.9.0

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-grist#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: v0.8.4...v0.9.0

v0.8.4

What's Changed

• [MRG] update notebooks for long contig names; add normalized snp figure (fig 11) by @ctb in #171
• [MRG] fix the ksize/moltype specified for sourmash gather by @ctb in #173
• [MRG] switch to using .sig.zip signatures; add summarize target by @ctb in #175
• [MRG] fix local genomes config file in docs by @mr-eyes in #182

Full Changelog: v0.8.3...v0.8.4

v0.8.3

What's Changed

• [MRG] add VCF-calculating code from #124 by @ctb in #165
• [MRG] fix and adjust gather-based known/unknown reporting by @ctb in #166
• [MRG] update mapping notebook to include SNP graph, and etc. by @ctb in #168

Full Changelog: v0.8.2...v0.8.3

v0.8.2

What's Changed

• [MRG] split identifiers on whitespace, not just spaces. by @ctb in #150
• [MRG] minor updates, incl. sourmash version updates. by @ctb in #160
• [MRG] compress output signatures by @ctb in #158
• [MRG] print out unknown config variables by @ctb in #161
• [MRG] add a flag to prevent metagenome download from SRA by @ctb in #157
• [MRG] add sourmash_database_threshold_bp to docs & config check by @ctb in #162

Full Changelog: v0.8.1...v0.8.2

v0.8.1

What's Changed

• [MRG] fix identifier munging for local databases by @ctb in #145

Full Changelog: v0.8.0...v0.8.1

v0.8.0

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 #125
• [MRG] extract the depth summary code from the Snakefile to a script by @ctb in #128
• [MRG] several minor updates and cleanup by @ctb in #129
• [MRG] support local genome collections (including private genomes) by @ctb in #130

Full Changelog: v0.7.4...v0.8.0

v0.7.4

Developer fixes:

• updated lxml (== 4.6.4) and python versions (>= 3.7, < 3.10)