v17.1.0

Highlights

• Improved data validation
  • New rules for VCF files and clinical files
  • Addition of a new flag --skip-database-checks in the genie validator cli to skip all validation rules requiring internal database access
• Added support for triggering integration tests via GitHub PR labels, enabling concurrent development

Validation Rule Updates

• [GEN-2324] Add VCF validation for expected columns by @rxu17 in #622
• [GEN-2407] Add new flag to genie cli to skip all validation rules requiring internal database access for local validator by @rxu17 in #628
• [GEN-2328] Add SAMPLE_CLASS and SAMPLE_TYPE validation for cfDNA by @rxu17 in #632, #634
• [GEN-2327] Set SAMPLE_CLASS to be a required column by @xindiguo in #633

Data Processing Changes

• [GEN-2537] Storing processed maf file first then upload to maf db by @rxu17 in #636

Technical Features

• [GEN-1654] Trigger integration tests via GitHub PR label by @rxu17 in #612
• [GEN-2332] Add workflow to automate the building of the genome nexus annotator by @rxu17 in #618

Bug Fixes

• [GEN-2375] Replace deprecated DataFrame.append with pandas.concat by @rxu17 in #620
• [GEN-2377] Remove set as index by @rxu17 in #621
• [GEN-2538] Fix docker build by pinning setuptools due to missing module pkg_resources by @rxu17 in #637

Documentation

• [GEN-2380] Update technical doc instructions for environment setup by @rxu17 in #623
• Update readme development instructions for genie onboarding by @rxu17 in #627
• Update package release steps by @rxu17 in #635

Other

• [GEN-2311] Deprecate dockerhub section in the technical docs by @rxu17 in #617
• [GEN-2368] Deprecate meta_fusions.txt by @rxu17 in #630
• [GEN-2326] Centralize where error reports get saved in Genie by @rxu17 in #629

New Contributors

• @xindiguo made their first contribution in #633

Full Changelog: v17.0.0...v17.1.0