v16.6.0

Highlights

• Automated the updating of Genome Nexus truststore used in maf processing to prevent ALL failed annotations

  • This greatly reduces the likelihood of having to start the pipeline all over again (maf processing is the 1st step of the pipeline)

• Improving cBioportal integration

  • Added structural variant (SV) column to gene panel matrix file

Data Processing Changes

• [GEN-1332] Added structural variant (SV) column to gene panel matrix files by @danlu1 in #587
• [GEN-1954] Added Transcript_Exon as new additional MAF column by @rxu17 in #592

Technical Features

• [GEN-1616] Automated update of Genome Nexus truststore by @rxu17 in #588
• [GEN-2027] Enabled mutation in cis process for staging by @rxu17 in #597
• Updated truststore update cadence by @rxu17 in #600

Bug Fixes

• [GEN-1759] Fixed bug with deploy GitHub job by @rxu17 in #585
• [GEN-1953] Resolved issue with moving MAF table to less restrictive project by @danlu1 in #595
• [GEN-2001] Set synapse query timeout for MAF table upload by @rxu17 in #596
• [GEN-2094] Used customized _copyRecursive to enable copying files with access restrictions by @danlu1 in #598
• [GEN-2210] Fixed setting of skip_mutationsincis flag for staging by @rxu17 in #603

Other

• Updated release package guidelines by @rxu17 in #586
• Updated local validator README by @rxu17 in #589
• [DPE-1253] Added PR description template by @danlu1 in #590
• Added mermaid flowchart diagram for the input to database / database to staging steps by @thomasyu888 in #591
• [GEN-1969] Updated retraction policy by @danlu1 in #593

Full Changelog: v16.5.0...v16.6.0