v2.2.12

Fix Dockerfile

Full Changelog: v2.2.11...v2.2.12

v2.2.11

What's Changed

• Fix distribution gff errors by @haessar in #55
  A lot of jobs were failing "at the final hurdle" during gff distribution. Traced it back to an earlier change made during gene splitting at gaps, where I'd neglected to ensure all "leaves" of affected transcript features were deleted as expected.

Full Changelog: v2.2.10...v2.2.11

v2.2.9

Release for Zenodo

Full Changelog: v2.2.8...v2.2.9

v2.2.8 - hotfix

Fix BRAKER output parsing bug

Full Changelog: v2.2.7...v2.2.8

v2.2.7 - hotfix

As BRAKER v3 uses TSEBRA, which appears to remove the gene scores, the filtering of gene models based on the AUGUSTUS_SCORE_THRESHOLD using genometools was broken. Therefore decided to remove that filtering process when parsing braker output (it still exists for base AUGUSTUS processes).

Full Changelog: v2.2.6...v2.2.7

v2.2.6 - hotfix

Full Changelog: v2.2.5...v2.2.6

v2.2.5

What's Changed

• Upgrade BRAKER to remove GM_KEY req by @haessar in #53

Full Changelog: v2.2.4...v2.2.5

v2.2.4 - hotfix

What's Changed

• install gt 1.6.3 from source by @haessar in #49

Full Changelog: v2.2.3...v2.2.4

v2.2.3 - hotfix

What's Changed

• Catch/ignore job breaking exception during gene splitting by @haessar in #48
  NOTE - requires genometools > v1.6.2

Full Changelog: v2.2.0...v2.2.3

Release v2.2.0

2.2.0 (2023-11-13)

What's Changed

• v2.2.0 by @haessar in #47

Highlights

• Extension of API/MIT conditional overlap logic
• Reference metadata and companion version now included in result outputs
• Allow bypass of gene filtering logic for invertebrate mitochondrial genes (i.e. Vectors)

Other changes

• max run time for BRAKER to prevent never-ending processes.
• Updated PFAM data
• Rename remaining orthomcl refs to orthofinder, and limit execution to just orthogroups

Full Changelog: v2.1.3...v2.2.0