Bakta

This is the 4th v1.2 patch release (v1.2.4) fixing a database download issue.

Bug fixes:
- fixed the database download/update logic by restoring an accidentally removed URL: https://github.com/oschwengers/bakta/commit/247a0475ecd7570e094e6c85f15c2f8893e88369 (Thanks andreaniml)

This is the third v1.2 patch release (v1.2.3) providing some minor improvements and a bug fix.

Compatible database scheme version: v3

Improvements:
- added several CI argument tests: https://github.com/oschwengers/bakta/commit/e26b5f56d1aa02563bc71ca6d6b9700c181c07fa https://github.com/oschwengers/bakta/commit/f5c57efd63fb2bdbfb9185fc765299652fdb159c https://github.com/oschwengers/bakta/commit/af20f66b133d5fc70eaaae04af4099eaa737c2c0 https://github.com/oschwengers/bakta/commit/dfc9a66cbec94727a4da10badbf8b688f91cff35 https://github.com/oschwengers/bakta/commit/a37b5b54237a046f655c1b95049cb17d80c8a65c
- added locus and locus-tag prefix argument checks: https://github.com/oschwengers/bakta/commit/842437b5050a23afbb5ce6c6708cae18d94efb77 https://github.com/oschwengers/bakta/commit/31fd72e7881aa23ad2c51496729ca0550b894540 https://github.com/oschwengers/bakta/commit/c530e4c1ad8bd0ba68c6302e04a507df546f4170 https://github.com/oschwengers/bakta/commit/8e27f6834beb4b028eacd8d0954237a15195755c https://github.com/oschwengers/bakta/commit/8c58851acebd01fc33e09dd291049e00384c1e60
- polished readme and error messages
- added citation information

Bug fixes:
- fixed the creation of a user defined tmp directory: https://github.com/oschwengers/bakta/commit/753e6e80d49ddfe285f6225c8f3347877bafe526

This is the second v1.2 patch release (v1.2.2) providing a couple of improvements and bug fixes.

Compatible database scheme version: v3

Improvements:
- set BLAST_USAGE_REPORT environment variable to `false` forestalling `blastn` to hang for 90 secs if no internet connection is available
- add a check for duplicated input sequence IDs: https://github.com/oschwengers/bakta/commit/888bb9b06bda62f88d8a93e0dfbd85eb7cf50e3e (Thanks joyn-sromero)
- add further SQLite URI parameters to improve read-only access: https://github.com/oschwengers/bakta/commit/e658a2ea2e0f48434eade93198d9c6c346480cb2
- synchronize Conda environment dependencies and runtime dependency version checks: https://github.com/oschwengers/bakta/commit/95ef71fd40dbeb471a3c45e04bc389ccf2ca08df https://github.com/oschwengers/bakta/commit/c516656661eaedaa933c1689a0ec6dd4ddc8267b
- add AMRFinder protein hits to dbxref outputs: https://github.com/oschwengers/bakta/commit/505a2ce8743eb227e8422567f779d6d3c46b33b3

Bug fixes:
- fix `NA` issue on HMM-only AMRFinder hits: https://github.com/oschwengers/bakta/commit/71e2dac3c17136e55c258dff8cf2cfe700b2c670 https://github.com/oschwengers/bakta/commit/e9ff01cead6524c4c96a09fec1d8bd7df144d23e (Thanks taylorreiter)

This is the first patch release (v1.2.1) merely fixing a wrong former version tag (v1.1.2).

This is the second minor release (v1.2.0) introducing user provided proteins as well as many improvements.

This is the first v1.1 patch release (v1.1.1) providing a couple of improvements and minor bug fixes.

Compatible database scheme version: v3

Improvements:
- added a revision & refinement logic for gene symbols: https://github.com/oschwengers/bakta/commit/539137be5cd82b7b01960b09f1a69e2a6536ae17
- added further CDS product revision rules: https://github.com/oschwengers/bakta/commit/f8ec2aa69c9b01da542e0cd49a4878bb6281be3f https://github.com/oschwengers/bakta/commit/1fcca891087e16d0ab5b6844ac21a230901e09d4 https://github.com/oschwengers/bakta/commit/8915af7d5fc81e5e7d306bbc8e1e18ca4c717b10 https://github.com/oschwengers/bakta/commit/626981bb9a385f890c8f817f45d7d31e75d8f50b https://github.com/oschwengers/bakta/commit/321391b1d0a336541c03732a28c95e99ca4dc0b6 https://github.com/oschwengers/bakta/commit/0d93c2fd0edf1affa22c172fbe87045bc16ec16f https://github.com/oschwengers/bakta/issues/69 (Thanks michoug)

Bug fixes:
- fixed AMRFinderDB issue in docker shell script: https://github.com/oschwengers/bakta/commit/e8253616dd37ad55ff61df64a7494253351692a2
- fixed `None` values of CDS `rbs_motif` attributes: https://github.com/oschwengers/bakta/commit/0727b2551207e1bf57514f3824572f004a11fd9e
- skip CDS annotation if no CDS are predicted: https://github.com/oschwengers/bakta/commit/3787e01a2e44eb5c80d6a19d8350a6bce3732415
- fix several CDS product revision rules