Aviary v0.13.0 introduces major dependency and database updates, experimental web-based run monitoring and results exploration, myloasm assembler support, GFA graph generation, RastQC-based QC reporting, and numerous pipeline stability fixes. This release updates SingleM to v0.21.3, GTDB-Tk to v2.7.2, and moves the taxonomy database stack to GTDB R232 latest release.
Key changes
- Updated SingleM to v0.21.3 and moved to the S6.5.0 GTDB R232 metapackage.
- Updated GTDB-Tk to v2.7.2 and the GTDB database to release232.
- Added an experimental Flask web interface for monitoring runs, exploring results, viewing taxonomy trees, inspecting bin quality reports, visualising assembly graphs, and exporting outputs.
- Added myloasm as a supported long-read assembler, alongside Flye.
- Added retention and generation of GFA assembly graph files for short-read and long-read assemblies.
- Replaced FastQC with RastQC for short-read QC reporting.
- Improved integration testing, including SingleM metapackage support and separated CPU/GPU test output directories.
- Fixed multiple workflow robustness issues, including symlink handling, compressed file support, missing dependencies, temporary directory creation, CUDA environment conflicts, NanoPlot concurrency, GTDB-Tk scratch usage, and isolate workflow compatibility.
- Updated isolate functionality with medaka
>=2.2.1and dnaapler>=1.0.0. - Improved resource handling for GPU and expensive tests.
Full Changelog: v0.12.0...v0.13.0