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@d-cameron d-cameron released this 21 May 07:36
· 119 commits to master since this release
v2.12.0
35270ee

New release to coincide with formal publication of VIRUSBreakend (https://doi.org/10.1093/bioinformatics/btab343).

** Temporary notice: Docker images are building/uploading. gridss conda package is in the process of being updated. This notice will be removed when the docker images and conda packages are available for usage.**

Critical packaging changes

  • .sh and .R suffix removed from all gridss tools.
    • You'll need to update your pipeline scripts or add symlinks (e.g. ln -s gridss gridss.sh)
Previously 2.12.0
gridss.sh gridss
virusbreakend.sh virusbreakend
virusbreakend-build.sh virusbreakend-build
gridss_annotate_vcf_kraken2.sh gridss_annotate_vcf_kraken2
gridss_annotate_vcf_repeatmasker.sh gridss_annotate_vcf_repeatmasker
gridss_extract_overlapping_fragments.sh gridss_extract_overlapping_fragments
gridss_somatic_filter.R gridss_somatic_filter
gridss.config.R gridss.config.R
libgridss.R libgridss.R
  • gridss/gridss:latest Docker image now includes tools and dependencies for running all GRIDSS tools including VIRUSBreakend (#473)
  • New gridss/gridss_minimal:latest docker image for running just gridss
  • New gridss/virusbreakend:latest docker image for running virusbreakend and virusbreakend-build

VIRUSBreakend

  • #484 Added VIRUSBreakend support for viral contigs in reference genome
    • By default, chrEBV and all NCBI viral contigs are considered viral reference contigs
    • Fixes missing EBV due to inclusion of NC_007605 in hs37d5 and chrEBV in hs38DH/GRCh38_full_analysis_set_plus_decoy_hla
  • Using default GRIDSS jvm heap size since Kraken2 needs more memory now that bacterial sequences are included
  • Added nodes.dmp to VIRUSBreakend database so downstream tools can look up the virus name from the .summary.tsv output
  • #446 Now immediately terminates instead of attempting to continue if one of the child processes does not complete successfully
  • Expanded documentation

Other changes

  • #494 Added support using the hmmer engine of RepeatMasker
  • #488 regenerating index files if they are zero size
  • Fixed gridss not exiting after usage message when no BAM supplied
  • Fixed broken --working_dir argument of gridss_annotate_vcf_repeatmasker
  • Fixed regression error causing assembly to be run even when the assembly output file already exists
  • Releases no longer depend on local environment and are built using a multi-stage Dockerfile
  • #489 removed unused RF VCF header
  • gridsscache files deleted if outdated
  • #491 Updated dependencies
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