Changes

Revision history for beacon2-cbi-tools:

2.0.12  2026-03-25

    - Refactored the Perl 5 wrapper to Python 3 while keeping the existing Perl internals in place
    - Updated CLI STDOUT formatting, colors, spinner behavior, and final messages
    - Added Python tests under 'tests/' and renamed integration data directory 'test/' to 'testdata/'
    - Updated README/docs generation to stop relying on 'pod2markdown'
    - Reduced install requirements to the core runtime dependencies and split docs dependencies into 'requirements-docs.txt'
    - Renamed 'scripts/' to 'deploy/'
    - Dockerfile: Updated the base image from Ubuntu 20.04 to Ubuntu 24.04

2.0.11  2025-12-23

    - STDOUT spinner is turned off when --debug or --verbose are used
    - Fixed persistent COLOR in SHELL after STDERR in Docker/HPC
    - BFF Browser: added clinician-friendly filters (Pathogenic clinicalRelevance, homozygous ALT), row counters, and visual highlighting

2.0.10  2025-05-15

    - Added 'tsv' mode to support SNP microarray data as input
    - Updated paths in 'scripts/02_test_deployment.sh'
    - Path to Java bin now can be set via config.yaml

2.0.9  2025-05-10
    - Added docs
    - Made STDOUT friendlier with UTF-8 emoji (turn off via --no-emoji)
    - Restored defaults to: mem=8GB, tmpdir=/tmp, dbnsfpset=all
    - VCF2BFF
      - Fixed error in assignment of 'clinicalRelevance' that was using 'CLINVAR_CLNSIGINCL' (i.e., haplotype-based) when present, instead of 'CLINVAR_CLNSIG'
        - Affected variant rate in CINECA_synthetic_cohort_EUROPE_UK1 (chr22 WGS VCF): 
          - Total variants: < 0.0003% (3 / 1,109,368)
          - ACMG-annotated variants: < 0.03% (3 / 10,580)
      - Added additional properties '_CLINVAR_CLNSIGINCL' and '_CLINVAR_ALLELEID' (if present) to the 'clinicalInterpretations' object
    - BFF2HTML
      - Added pattern 'MODERATE' for fetching these annotated variants in 'bff2html'.
      - Display only one 'clinicalRelevance' per variant instead of one per 'clinicalInterpretation'
      - Fixed issue with assigning URLs to the comma-separated ‘ClinVar’ column

2.0.8  2025-03-22

    - The CRG FTP site has reached end-of-life after three years of availability
      - External files moved to a new location; download script updated accordingly
      - External datasets are now downloaded outside the container, simplifying data persistence
    - Repository renamed to 'beacon2-cbi-tools' ([C]NAG [B]iomedical [I]nformatics)
    - Repository transferred to @CNAG-Biomedical-Informatics organization
    - Added support for arm64 (Apple Silicon / M-based Macs) architectures
    - 'mongosh' is now installed via apt
    - Updated Dockerfile
    - BEACON => BFF-TOOLS:
      - 'lib/BEACON/ => 'pipeline/' and 'Beacon.pm' => 'Tools.pm'
      - 'mongodb' mode renamed to 'load'
      - Added 'validate' mode runs 'utils/bff_validator/bff-validator'
      - Now accepts pre-annotated VCFs using `annotate: false` in YAML configuration (requires mandatory ANN fields)
      - Added an 'examples' directory featuring hg38 (GRCh38)
      - Added spinner for interactive execution of 'bin/bff-tools'
      - Added basic tests in 't/' directory
      - Internal scripts moved from 'lib/BEACON/bin/' to 'pipeline/internal/{complete,partial}/'
      - Updated 'bin/config.yaml' with placeholder `{base}`
      - Added $version, $java, and $arch information to 'log.json'
      - Updated tools versions:
        - 'bcftools': 1.15.1 -> 1.21-103
        - 'mongo-database-tools': ubuntu2004-100.5.1 -> ubuntu2204-100.9.4
        - 'ClinVar' from clinvar_20211218* to clinvar_20250312*
      - VCF2BFF:
        - Renamed legacy Perl modules under pipeline/
        - Added t/ and debugging mode 'bff-pretty'
        - Now reads 'annotatedWith' from external 'config.yaml' (fixed typo: toolreferences.dbSNSFP -> dbNSFP)
        - Added Sequence Ontology (SO) terms for calculated variant consequences:
            https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html

2.0.7  2025-02-22
    - Moved 'browser/web' to 'utils/bff_browser/static/assets'
    - Added argument '-projectdir-override' to enable external assignment of id (e.g., Celery)
    - Renamed internal parameter from 'ncpu' to 'threads' and option '-n' to '-t'

2.0.6  2025-01-15
    - Created a Flask app for 'utils/bff_browser' (currently in development)
    - Changed 'bff2html' to output JSON arrays instead of NDJSON for files like 'foo.json' (e.g., 'exome.json')
    - Updated 'docker-compose.yaml' to reflect recent changes
    - Renamed 'bff_api' to 'bff_portal' and added a basic frontend interface for the API

2.0.5  2025-01-07
    - The 'config.yaml' for the 'beacon' script is now pre-formatted for the Dockerized version
    - Renamed 'testdata/param.in' to 'testdata/param.yaml'
    - Enforced Browser HTML display using Python3's default HTTP server

2.0.4  2024-12-03
    - Moved 'beacon' script to 'bin/beacon' and updated paths.
    - Reorganized repo in folders

2.0.3  2024-05-24
    - Added Unicode support to 'utils/bff_validator'

2.0.2  2024-02-07
    - Updated 'docker-compose.yml'.
    - Changed 'config.yml' to enable connecting to @mongo from within 'beacon2-ri-tools' container

2.0.1  2024-01-22
    - Updated contact email to @cnag.eu.
    - 'utils/bff-validator': Adjusted STDOUT printout details
    - 'test': Sorted 'frequencyInPopulations' by key in 'genomicVariationsVcf.json.gz'
    - Docker Hub location updated to 'manuelrueda/beacon2-ri-tools'
    - Moved 'BEACON' to 'pipeline/BEACON'
    - Fixed 'Dockerfile':
        - Changed base image from 'ubuntu' to 'ubuntu:20.04' (thanks to SJD folks)

2.0.0  2022-08-18
    - Stable version released along with the accompanying paper:
        * _Bioinformatics_, btac568, https://doi.org/10.1093/bioinformatics/btac568
    - Works with [Beacon v2.0.0](https://github.com/ga4gh-beacon/beacon-v2/releases/tag/v2.0.0) specification