- Fixed Zero divison error when there is no allele depth in the variant calls (#43)
- Updated Config
- Fixed Pharmacat memory bug
- Major change to the process flow
- Updated pharmact to v2.12.0
- Updated ReadMe.md
- Updated QC text in the report
- Added pharmCAT module to the pipeline
- Updated DPYD HapB3 haplotype related rsids (rs75017182 and rs56038477)
- Main target bed regions are padded with 20bp up and down stream
- The report will now include a telephone number for medical information support related to its contents.
- Added and updated various features:
- Added license and workflow image.
- Implemented nf-core style stubs.
- Completed modularization of the pipeline with external arguments, singularity images, and configs.
- Introduced panel/WGS profiles.
- Addressed issues with variant calling for multiple samples and parallelization.
- Variant calling and analysis improvements:
- Added variant calling with SENTIEON/GATK, including variant filtration and annotation.
- Important updates and fixes:
- Corrected the NUDT15-3 rsID issue.
- Updated recipe files and references for HG38 in configs, improving variant filtration.
- Various report enhancements:
- Fixed report warnings and updated report generation logic.
- Improved report format, including a new logo, CSS updates, and added a gene table.
- Added quality control comments and sample-specific MultiQC reporting.
- Introduced a new Python-based reporting module, replacing the older R-based module.