Releases: BU-ISCIII/buisciii-tools
Releases · BU-ISCIII/buisciii-tools
Release list
BUISCIII/buisciii-tools v2.3.3
Credits
Template fixes and updates
- Added parallelization to IRMA's 99-stats summary creation. #648
- Fixed major error while filtering IRMA's vf files. #649
- Fixed wgstrio 99-stats lablog to prevent OutOfMemoryError on WGS samples. #654
- Fixed wgstrio folder template structure #655
- Updated recommended Nextflow version in taxprofiler lablog #655
- Fixing AF filtering and results symlinks in wgstrio template #659
- Fixed column selection, now selects MAX_AF in wgstrio template #660
- Fixed QSslSocket and wkhtmltopdf errors in bioinfo-doc PDF generation #662
- Make VEP header generation dynamic and remove static template dependency [#664] (#664)
- Updated blast database with new assemblies downloaded in March 2026 #665
- Added numeric sample ID validation for samplesheet.csv in assembly lablog #667
- Updated
wgstrio,exometrioandrnaseqtemplates to generate OmicsExplorer-compatible outputs. #668 - Updated blast database location to refgenie directory #683
- Add trim_poly_x fastp arg to assembly config #685
- Updated A__N1 and A__N2 subtype results in flu_type_refs.txt #687
- Updated new paths to refgenie databases in databasesheet.csv of taxprofiler #689
- Updated viralrecon's config file #691.
- Updated the services.json file's structure, so that an auxiliary cleaning file is used by the clean module if applicable #692.
- Optimized annotation wgs & exome #695
- Updated several software versions #696
- Updated nextclade checks for IRMA and viralrecon #697
- Enabled micromamba env activation when launching a script #699
- Updated kaiju conf for taxprofiler #701
Modules
Implementation
- Added DROP as a new service, including automatic input generation, module-specific adaptations and standardized result processing. #668
- Created viralrecon_clean.py, an auxiliary file to clean unnecessary files from viralrecon service #692.
Added enhancements
- Improved clean module so that an aux cleaning file is employed for specific services if applicable #692.
- Improved HTTP error handling in drylab_api module and fixed fix-permissions so that it does not break given insufficient permissions #694.
- Implemented date filtering for research in archive, improved logging and error handling #700
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.3.2
Credits
Template fixes and updates
- Fixed tbprofiler
delivery_mdandresults_mdpaths inbuisciii/templates/services.json#640 - Fixed new taxprofiler pipeline yaml filename in versions lablog #641
- Fixed grep subtype anchor in IRMA variant-calling lablog to correctly filter Influenza B references #644.
- Updated assembly's RESULTS lablog in accordance to nf-core/bacass' 2.5.0 version #645.
Modules
Added enhancements
Fixes
Changed
Removed
Requirements
BUISCIII/buisciii-tools v2.3.1
Credits
Template fixes and updates
- Modified
create_assembly_stats.Rto group by sample in viralrecon template #631. - Fixed error handling in finish module and automatic logging for new_service #632.
- Solved symlink path for TBProfiler results lablog #634
Modules
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.3.0
Credits
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_lintnow uses Python 3.10 #615
BUISCIII/buisciii-tools v2.2.13
Credits
Template fixes and updates
- Updated sftp_user.json #568.
- Fixed the parse_ariba.py script and stored in the 99-stats folder from the CHARACTERIZATION template #568.
- Updated IRMA template to comply with new sample id format in relecov analysis 578
- Fix pkg_resources installation error and pin bacass version in Assembly template 579
Modules
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.12
Credits
Template fixes and updates
- Fixed IRMA's 99-stats lablog to take host reads from samtools stats instead of kraken #564.
- Fixed sgene_metrics.sh to handle warnings properly #565.
Modules
- Fixed finish module so that the clean module is run correctly #564.
- Fixed bioinfo_doc module so that a text file can properly be used for email notes #564.
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.11
Credits
Template fixes and updates
- Added micromamba environment PikaVirus_dev_2.6 to file hpc_slurm_pikavirus.config #535.
- Changed analysis_date in create_summary_report.sh to take properly dates from RSV services when using viralrecon #540.
- Fixed date formats for IRMA's template and excel_generator.py #549.
- Fixed the way whether samples are paired or single-end is detected #550.
- Removed pseudo_aligner parameter from RNASeq's lablog and added all missing symlinks in its RESULTS's lablog #552.
- Updated scratch.py and main.py to properly handle custom paths and temporary directories #555.
- Updated create_summary_report.sh to transform negative values into 0 #556.
- Updated the assembly stats script to handle files in RAW properly and when quast results are not available for any sample #557.
Modules
- Fixed clean module to handle subpaths stated in services.json #543.
- Fixed bioinfo_doc module to be able to indicate type (service_info or delivery) via CLI #558.
- Fixed the bioinfo_doc module to properly ask for email text notes and the scratch module to use proper scratch_tmp_path #559.
Added enhancements
- Added new script to download multiple SRA entries in fastq format when necessary #551.
Fixes
Changed
- Modified bu-isciii > buisciii for all commands in README text #548.
Removed
BUISCIII/buisciii-tools v2.2.10
Credits
Template fixes and updates
- Redefinition of analysis_date and lineage_analysis_date based on mapping folder and DOC config in viralrecon's template #523.
- Fix analysis_date and lineage_assignment_date format in create_summary_report.sh #525.
- Created a new script to correctly merge all nextclade results into one .csv file in IRMA's template, apart from updating lablog_irma_results with new symlinks to relevant files #526.
- Adapted create_summary_report.sh to handle multiple references and add lineage columns to pangolin .csv only if they do not exist yet #530.
Modules
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.9
Credits
Template fixes and updates
- Updated create_summary_report.sh to properly handle single end reads #509.
- Fix relative path handling in snpeff/snpsift annotation #509.
- Added sed to lablog_bam2fq so that _R1.bam is removed and the variable sample is created properly for those sample ids having several underscores (i.e. EPI_ISL_666)#490
- Update IRMA 99-stats lablog to raise Error if taxprofiler results are missing #515.
- Added a new lablog to create a .csv file for software versions in IRMA's template #514.
- Fixed wrong variable definition in IRMA's 99-stats lablog and added Nextclade's info into viralrecon's create_summary_report.sh script to be added into the mapping_illumina report #518.
- Added virus_sequence variable into IRMA's 99-stats lablog for the creation of the summary stats report #519.
Modules
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.8
Credits
Template fixes and updates
- Updated snippy template, now using a modified version of snippy with different low coverage masking#489
- Update PlasmidID Report Generation to Output Summary by Sample #483
- Update of the execution of summary_report_pid.py in plasmidID lablog #484
- Added
sort -uto wgs_metrics_all.txt file generation command in 99-stats lablog (snippy template) #494 - Avoided error messages when running 99-stats lablog several times (snippy template) #495
- Added Nextclade, variant calling and stats extraction scripts into the IRMA template #499.
- Added flu_type to summary_stats (IRMA template) #501.
- Fixed errors in IRMA template and fixed errors in irma2vcf script #500
- Modified artic bed version in lablog_viralrecon for SARS-CoV-2 analysis #505
Modules
Added enhancements
- Implemented multi-attachment support in Bioinfo-doc email sending workflow #488
- Added kmerfinder to snippy template #498
Fixes
Changed
- Expanded the maximum width of email body to 1000px for better desktop display #488
- Corrected the logo URL to use a direct raw link for proper rendering in email clients #488