Releases: Clinical-Genomics-Lund/bonsai
Releases · Clinical-Genomics-Lund/bonsai
Release v0.8.0
Added
- Added select all variants button to tbprofiler and SV cards in Variant report view.
- Added button to the groups view for adding selected samples to group.
- Added button to the group view for removing selected samples from group.
- Added column with comments indicator to group and groups view.
- Added foundation for testing API routes.
- Added test for Allele cluster service.
Changed
- Genome coverage plot to interactive and have an y-range of 0 to 100.
- Use data-tables instead of w2ui for samples tables.
- Improved error handling of allele cluster service.
- Removed swedish characters from LIMS export output.
Fixed
- Fixed highlight of displayed sample in the dendrogram on the sample view page.
- Fixed formatting of grapetree metadata that could crash the frontend.
- Fixed crash in Allele cluster service when clustering samples with the same profile using MsTree or MsTreeV2.
v0.7.0
[v0.7.0]
Added
- Can configure SSL verification and usage of SSL certs for API requests from frontend.
- Added cards ShigaPass result and function to tag Ecoli and Shigella spp with ShigaPass result.
- Added option to filter variants on WHO class and variant type in the variants view.
- Added button to reset variants filter on the variants view.
- Added support for more IGV annoation file formats.
Changed
- Bonsai now uses sample ids created by Jasen to identify unique samples.
- Updated PRP to version 0.10.1
- Improved installation instructions.
- Updated requests to version 2.32.0
- Added startup commands to minhash and allele clustering services Dockerfiles.
- Use pydantic-settings for config management in frontend.
- Updated the samples tables to make sample name, sample id, and major spp searchable.
- Truncate long tbprofiler variant names and show full name on hover.
- Fixed issue that could prevent IGV from loading.
- Updated IGVjs to version 3.0.2
- Updaed how AMR variants are displayed on the sample view page. All varians are displayed if no variant have been processed, otherwise only show passed resistance yielding variants.
Fixed
- Fixed misalignment of the checkbox in the samples table in the group and groups view.
- Fixed bug in the TB lineage card that could crash the frontend.
- Fixed an issue where samples without MLST profiles could crash GrapeTree.
- Fixed removal of new ChewBBACA alleles call info codes.
v0.6.0
Added
- Added source of tbprofier db entry as badge to result card.
- Added species and phylogroup prediction from Mykrobe.
Changed
- Updated IGVjs to version 2.15.11
- Updated PRP to version 0.8.3
- Updated the formatting of the results table in the tbprofiler card.
Fixed
- Fixed bug in generating mongodb URI
- Fixed crash if vcf type was not recognized
- Fixed bug that prevented samples to be reomved from the basket.
- Improved error handling if a sample could not be removed from the basket.
v0.5.0
v0.4.1
[v0.4.1]
Compatible with JASEN v0.6.0
Added
- Display LIMS id in samples view
Changed
- Sample name is being displayed instead of sample id on the samples view
- Dockerfile chown step for api and frontend
Fixed
- Fix minhash sample id lookup by storing sample_id as signautre name when signature is written to disk.
- Links to a sample from the samples tables now works when Bonsai is hosted under a sub-path
- Fixed so the samples could be added to the minhash index
- Fixed nameing of signature sketches and updating filename
- Fixed broken URL that prevented finding similar samples
- Fixed storing of selected samples in browser session that prevented samples to be added to the basket from the groups view.
- Fixed broken URLs in dendrogram in samples view
- Fixed crash when reading empty sourmash index
- Fixed crash in resistance/variants view when a samples did not have SNVs or SV variants
v0.4.0
[v0.4.0]
Added
- Added Sample name, LIMS ID, and Sequencing run as selectable columns
- Sample name in sample view table links to sample
- New upload script (upload_sample.py) that takes a upload config in YAML format as input
Changed
- Sample id is assigend by concating lims_id and sequencing_run
- Sample id is not displayed by default
- API route POST /samples/ returns sample_id
- Removed upload_sample.sh
v0.3.0
Release version 0.3.0
Added
- Add button to remove samples from the group- and groups view.
- Added view for analyszing variants with filtering
- Added IGV genome browser integration to variant analysis view.
- Bonsai support display of SV and SNV variants.
- A user can classify variant as accepted or as rejected based and annotate why it was dissmissed.
- A user can annotate that a variant yeilds resistance to additional anitbiotics
- Placeholder Export to LIMBS button to the sidebar in the variants view
- Added CLI command for exporting AMR prediction to a LIMS tsv file
Fixed
- 500 error when trying to get a sample removed from the database
- Frontend properly handles non-existing samples and group
- Fixed typo in similar samples card that caused invalid URLs
- Fixed default fontend config to work with default docker-compose file
Changed
- Removed "passed qc" column from tbprofiler result
- Changed default app port to 8000 and api port to 8001
Release v0.2.1
Added
- Bulk QC status dropdown in group view
Fixed
- Fixed crash when clustering on samples without a MLST profile
- Fixed bug that prevented adding samples to the basket in groups without "analysis profile" column
- Fixed issue that prevented finding similar samples in group view
Changed
- Display the sum of kraken assigned reads and added reads in spp card by default.
- Froze uvicorn to version 0.25.0
- Updated fastapi to version 0.108.0
Release v0.2.0
Added
- Improved output of create_user API CLI command
- bonsai_api create-user command have options for mail, first name and last name.
- Open samples by clicking on labels in the similar samples card in the samples view.
- Optional "extended" HTTP argument to sample view to view extended prediction info
Fixed
- Fixed crash in create_user API CLI command
- Resistance_report now render work in progress page
- Removed old project name from GrapeTree header
- Fixed issue that prevented node labels in GrapeTree from being displayed.
Changed
- The role "user" have permission to comment and classify QC
- Updated PRP to version 0.3.0
v0.1.0
[v0.1.0]
This is the first beta release of Bonsai.
The release include the following features,
- Multi user results visualization
- Support for Jasen v0.3.0
- View resistance and virulence prediction results
- Find similar samples using MinHash distance
- Cluster multiple samples on MinHash, cgMLST, and MLST
- Organize samples in groups and customize which information to display
- Annotate samples using comments and QC evaluation