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v2.3.1

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@github-actions github-actions released this 13 May 09:44
· 241 commits to main since this release
v2.3.1
90850f1
  • 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
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