v2.5.1.0

What's Changed

• GitHub Actions runner ubuntu upgrade 20.04 -> 24.04 by @tomkinsc in #51
• Add CLAUDE.md and fix TestFilterLastal for last v1648 by @dpark01 in #53
• viral-core 2.3.3 to 2.5.1 by @dpark01 in #54

Full Changelog: v2.2.5...v2.5.1.0

v2.2.5

What's Changed

• update viral-core 2.2.4 -> 2.3.1 (w/ python 3.8 -> 3.10) by @tomkinsc in #44
• bump viral-core version 2.2.1 -> 2.3.3 by @tomkinsc in #50
• Adding arbitrary parameters to blastn_chunked_fasta function by @golu099 in #46
• update coveralls action; bump actions python to 3.10 by @tomkinsc in #48

Full Changelog: v2.2.4.2...v2.2.5

v2.2.4.2

What's Changed

• Adding kraken output perl scripts by @golu099 in #45

Full Changelog: v2.2.4.1...v2.2.4.2

v2.2.4.1

No code changes -- v2.2.4.0 was misspelled initially, breaking docker builds. This is simply another tag of the same commit.

v2.2.4.0

What's Changed

• add metagenomics.taxlevel_plurality by @dpark01 in #42
• docker build fix and filter_taxids_to_focal_hits fix by @dpark01 in #43

Full Changelog: v2.2.3.0...v.2.2.4.0

v2.2.3.0

What's Changed

new functionality / software updates

• bump diamond, kraken2, krona versions by @dpark01 in #32
• Updating Docker with Lydia's Perl Scripts by @golu099 in #36
• update docker base image to v2.2.3 of viral-core; Update conftest.py to account for breaking changes in the newer version of pytest by @tomkinsc in #41

build mechanics fixes and updates

• migration from Travis CI to GitHub Actions by @tomkinsc in #31
• update python modules evaluated for test coverage by @tomkinsc in #38
• rename test action in CI by @tomkinsc in #39
• change TravisCI badge to Actions badge in readme by @tomkinsc in #40

New Contributors

• @golu099 made their first contribution in #36

Full Changelog: v2.1.33.0...v2.2.3.0

v2.1.33.0

What's Changed

• kraken2 build fix for protein dbs by @dpark01 in #22
• bump viral-core 2.1.20 to 2.1.33 by @dpark01 in #22
• fix sphinx/rtd builds

Full Changelog: v2.1.20.0...v2.1.33.0

v2.1.20.0

Update viral-core to 2.1.20 (picard, samtools, pysam, zstandard)

v2.1.16.0

• bump viral-core to 2.1.16

v2.1.12.1

Changes:
taxon_filter.py::deplete(): revertBam is now a mandatory rather than optional positional argument