BUISCIII/buisciii-tools v2.3.0

Credits

• Victor Lopez
• Pau Pascual
• Magdalena Matito
• Juan Ledesma

Template fixes and updates

• Updated taxprofiler version in lablog #584.
• Fixed snippy folder in iqtree's lablog #584.
• Fixed minor mistake in generate_summary_outbreak.py #584.
• Enhanced differential_expression.R when reporting results #584.
• Updated the lowfreq_panel template #586.
• Updated sftp_user.json to add mcoiras #595.
• Replace MTBseq with TBProfiler in README.md #597.
• Replace MTBseq with TBProfiler in templates/services.json #598.
• Updated emmtyper's lablog #603.
• Updated bacass version in assembly's template #604.
• Updated sftp_user.json to add bdandres to LabInmunology #605.
• Refactor MTBseq template for TBProfiler pipleine with its lablogs #607
• Added new authors contact in pyproject.toml #607
• Update tbprofiler assets/reports/md markdown file and tbprofiler assets/reports/results markdown file #607
• Added new BLAST database created in July 2025 #608
• Added hgil and Labviruspapiloma to sft_user.json #609
• Updated taxprofiler's lablog so that Bowtie2 uses an already built index #612.
• Updated viralrecon's lablog to avoid exiting when the refgenie env is not loaded, even when it actually is #613.
• Completed service info in services.json #619.
• Updated sftp_user.json to add lorena.pozo to labantibiotics #620.
• Replaced conda by the corresponding micromamba's env in amrfinderplus's lablog #621.
• Removed exomiser.html part from trios' results md and fixed wrong image paths in exomeeb results md #622.
• Added new exometrio bed files #624.
• Fixed minor mistake in chewbbaca's lablog #625.

Modules

Added enhancements

• Fixed new-service to properly check MD5 files when samples do not belong to the same run #583.
• Implemented logging and error handling in buisciii-tools #619.
• Replaced pkg_resources by importlib.metadata due to pkg_resources being deprecated #619.

Fixes

Changed

Removed

Requirements

• Updated GitHub action: python_lint now uses Python 3.10 #615