Bakta

This is the third v1.3 patch release (v1.3.3).

This is a quick fix reverting an `alive-progress` version bump to `v2.1.0` that is not available via Conda. Sorry for any inconvenience caused.

Bug fixes:
- fixed a file permission issue on bakta_db update: https://github.com/oschwengers/bakta/commit/de42d3fad5cbe574b6c2b7a643ea246c247a2017
- pinned `alive-progress` version to `v1.6.2` to fix potential API errors: https://github.com/oschwengers/bakta/commit/dbc79acc40b3999da916f2aaa319e2de3c432db0 https://github.com/oschwengers/bakta/commit/60ac3ed02537628bb9264d18e16080e4a9ee5b54

This is the second v1.3 patch release (v1.3.2).

Bug fixes:
- fixed a file permission issue on bakta_db update: https://github.com/oschwengers/bakta/commit/de42d3fad5cbe574b6c2b7a643ea246c247a2017
- bumped alive-progress version to >=v2.1.0 to fix potential API errors: https://github.com/oschwengers/bakta/commit/dbc79acc40b3999da916f2aaa319e2de3c432db0

This is the first v1.3 patch release (v1.3.1).

Bug fixes:
- fixed the locus-tag checks: use a more relaxed format as default and INSDC restrictions on `--compliant`: https://github.com/oschwengers/bakta/commit/e2651c3c7c85efbbceacff1ac28482b3c636b536 (Thanks taylorreiter)
- skip `/pseudo` annotated genes in `--proteins`-provided GenBank files: https://github.com/oschwengers/bakta/commit/0f0165d0909ef26be29477751db301e68754f233 (Thanks Charlotte Reuschel)

This is the third minor release (v1.3) introducing a new feature and many improvements and bug fixes.

Compatible database scheme version: 3

New features:
- prediction of signal peptides via [DeepSig](https://github.com/BolognaBiocomp/deepsig): #32 (Thanks Anna-Rehm)

Improvements:
- provide summary with genome & annotation statistics as `.txt` file: 88 (Thanks hkaspersen)
- accept user provided proteins in GenBank format: 89 (Thanks Tonny-zhou)
- removed alignment gaps (`-`) in input sequences: 87 (Thanks RotimiDada)
- improved sORF overlap filter runtime performance: https://github.com/oschwengers/bakta/commit/cb204fbe52539abd92059b67b08b5f3352dea0b0
- improved outputs: https://github.com/oschwengers/bakta/commit/76e07a4db073bf839a2280e8fad1951d44e6c9e8 https://github.com/oschwengers/bakta/commit/90bfe99c65565036c0943e70fd9daa4d2321f610
- added more checks & tests: https://github.com/oschwengers/bakta/commit/b779e1fda82302e9156af0c1be9a7285e263c21d https://github.com/oschwengers/bakta/commit/4e6c35d3177977e9cec9bcf6cc86116f55cdd590 https://github.com/oschwengers/bakta/commit/f4103f09b7dc6edb49164e82a83a9b931d42eee6 https://github.com/oschwengers/bakta/commit/08ebb037bca1e976d102fe293d775a70b80ebd36 https://github.com/oschwengers/bakta/commit/1672a876141711f22d1cc8dd930a6f397458616d https://github.com/oschwengers/bakta/commit/26a8ed2f30eff456b808f62b0646039f566ff3b7
- added `--gram` to CWL file: https://github.com/oschwengers/bakta/commit/22463196c55bb93f20f6161ade76512a0bb36b2e

Bug fixes:
- fixed tmRNA predictions that cross sequence origins: 90 (Thanks LuisFF)
- moved oriC/T/V product to Note in INSDC and compliant GFF3 outputs: https://github.com/oschwengers/bakta/commit/2f5cb1dae8da57c6d00dfbe66c0b3d48769b128e https://github.com/oschwengers/bakta/commit/716302e63b66c34a0e30bcea83c8818b6a0d2255 https://github.com/oschwengers/bakta/commit/5e1a0d831fa4d948aa459a5b8340f2a18afa2a6c
- fixed sequence description on Fasta import: https://github.com/oschwengers/bakta/commit/bfdf67f53ed0e3995a4cdaa8c227e12c9b122848
- fixed Fasta import log error: https://github.com/oschwengers/bakta/commit/52096727d857d44e98cfbb821094dbc8853b4a8b
- fixed EDAM out types in CWL file: https://github.com/oschwengers/bakta/commit/a1a0ad116f1a0e8133aa41877f3b67af599820a6

And of course all improvements and bug fixes from all v1.2.x patch releases.

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