Changelog

v2.4.0

Breaking change: Removed bed_variant_hotspots in favor or annotation_criteria
Breaking change: Variants are now filtered using the filter_criteria file
Breaking change: Add mutalyzer_hgvs_parser to the conda environment
Breaking change: Update the json output format
Breaking change: Update Snakemake to version 8
Fix a bug with the Java runtime environment for Picard
Fix a bug with caching of report assets introduced in snakemake 8
Fix a bug with structural variants missing effect prediction
Add an option to specify variant_allele_frequency for snv-indels
Speed up VarDict by running with 8 threads
Speed up VarDict by sorting the call_regions.bed file
Run VEP with either vep_cache or just the gtf/fasta files as database
Update picard from 2.27.4 to 3.3.0
Update cutadapt from 4.6 to 5.0
Update sequali from 0.9.1 to 0.12.0
Update star from 2.7.10b to 2.7.11b
Update MultiQC to 1.27.1

Breaking change: The bed_variant_call_regions option has been removed, variants are now called for all genes present in the gtf file.
Breaking change: Add graphviz/dot as a dependency (developer only).
Fix a rare bug where different modules use the same MultiQC file list.
Fix a bug with filtering VEP records that contain multiple population. frequency records for a single variant.
Add ability to generate configurations for each module using the utilities/create-config.py script.
Update the hotspot regions reference file.
Update the blacklist of known artifacts.
Remove various superfluous plots from the MultiQC report.
Add expression module
- Add optional input strandedness to the sample configuration.
- Add json output file for the expression module.

Fix a bug with the maximum population frequency, this was accidentally set to 5% (it is now 1%)

Breaking change: Remove the JSON output for the qc-seq module (this has been replaced by a MultiQC report)
Breaking change: Add sample name to STAR counts table * Fix a bug where the trimmed FastQ files are not removed when no longer needed
Automatically remove _STAR temporary folders
Change PDF report cover image
Change PDF report to add bookmarks under chapter variant
Change PDF report to sort the genes of interest alphabetically
Change PDF report to remove the “Sequencing Results” section (this has been replaced by a MultiQC report)
Replace FastQC with Sequali
Update Cutadapt to 4.6
Update MultiQC to 1.22
Update snakefmt to 0.10.0 (developer only)
Update black to 24.3.0 (developer only)

Change PDF report to increase space for the HGVS description in “Results Overview” table

Fix a bug where long HGVS descriptions make the “Results Overview” table overflow the page

Breaking change: Deprecate option fusion-partners, in favour of report_genes, which points to a list of fusion genes to report
Fix a bug with inconsistent config setting blacklist in snv-indels
Fix a bug where unmapped reads are not included in STAR output file
Replace StarFusion and FusionCatcher with Arriba
Replace VarScan variant caller with VarDict
Replace GSNAP aligner with STAR
Update VEP to 108.2
Update Picard to 2.27.4
Update FastQC to 0.11.9
Update Cutadapt to 4.1
Change PDF report to remove the run name
Change PDF report to remove variants plots
Change PDF report to show allele frequency as a percentage
Use multiple threads for Cutadapt, and reduce the compression of output files
Add additional genes of interest
- SRSF2
- SF3B1
- U2AF1
- BCOR
- STAG2
- ZRSR2
- EZH2
Filter fusion results based on fusion partners
Add fusion plots from Arriba
Add default blacklist with common false-positive variants
Add support for variant blacklist in VEP hgvsc format
Add script to generate a configuration file
Add pipeline to generate reference files
Add per-module configuration options
Add support for PEP sample configuration
Add support for Snakemake 7.8.5
Use MANE select transcript for all genes