broadinstitute/gatk 4.2.4.1

4.2.4.1 the log4j strikes back

on GitHub

Download release: gatk-4.2.4.1.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.2.4.1 release:

• Fix more newly discovered log4j2 vulnerabilities. Now that people are paying attention they are finding all sorts of things.

Full list of changes:

• Build System

  • Upgrade our build from Gradle 5.6 to the newest 7.3.2 (#7609)
  • This fixes some gradle bugs which were blocking development

• GenomicsDB

  • Update to genomicsdb 1.4.3 (#7613) which fixes #7598
  • Fix bug which caused --max_alternate_alleles to be ignored when using GenomicsDB (#7576)

• Miscellaneous Changes

  • Update .dockstore.yml (#7595)
  • Fix developer doc in AS_RMSMappingQuality (#7607)

• Dependencies

  • Update log4j to 2.17.1 (#7624)(#7615)
  • Upgrade to Barclay 4.0.2. (#7602)
  • Update to genomicsdb 1.4.3 (#7613)