Skip to content

Version 4.61: ClinVar submission simplified, inheritance model colors, and more custom report types
Compare
Choose a tag to compare
@dnil dnil released this 24 Nov 10:03
· 1229 commits to main since this release
v4.61
a3268d2
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

[4.61]

Added

  • Filter case list by cases with variants in ClinVar submission
  • Filter case list by cases containing RNA-seq data - gene_fusion_reports and sample-level tracks (splice junctions and RNA coverage)
  • Additional case category Ignored, to be used for cases that don't fall in the existing 'inactive', 'archived', 'solved', 'prioritized' categories
  • Display number of cases shown / total number of cases available for each category on Cases page
  • Moved buttons to modify case status from sidebar to main case page
  • Link to Mutalyzer Normalizer tool on variant's transcripts overview to retrieve official HVGS descriptions
  • Option to manually load RNA MULTIQC report using the command scout load report -t multiqc_rna
  • Load RNA MULTIQC automatically for a case if config file contains the multiqc_rna key/value
  • Instructions in admin-guide on how to load case reports via the command line
  • Possibility to filter RD variants by a specific genotype call
  • Distinct colors for different inheritance models on RD Variant page
  • Gene panels PDF export with case variants hits by variant type
  • A couple of additional README badges for GitHub stats
  • Upload and display of pipeline reference info and executable version yaml files as custom reports
  • Testing CLI on hasta in PR template

Changed

  • Instructions on how to call dibs on scout-stage server in pull request template
  • Deprecated CLI commands scout load <delivery_report, gene_fusion_report, coverage_qc_report, cnv_report> to replace them with command scout load report -t <report type>
  • Refactored code to display and download custom case reports
  • Do not export Assertion method and Assertion method citation to ClinVar submission files according to changes to ClinVar's submission spreadsheet templates.
  • Simplified code to create and download ClinVar CSV files
  • Colorize inheritance models badges by category on VariantS page
  • Safe variants matching badge more visible on case page

Fixed

  • Non-admin users saving institute settings would clear loqusdb instance selection
  • Layout of variant position, cytoband and type in SV variant summary
  • Broken Build Status - GitHub badge on GitHub README page
  • Visibility of text on grey badges in gene panels PDF exports
  • Labels for dashboard search controls
  • Dark mode visibility for ClinVar submission
  • Whitespaces on outdated panel in extent report
Assets 2
Loading