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Chromograph and Beacon integration. Container deployment files

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@northwestwitch northwestwitch released this 28 Jan 14:08
v4.28
28d6f50
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[4.28]

Added

  • Chromograph integration for displaying PNGs in case-page
  • Add VAF to cancer case general report, and remove some of its unused fields
  • Variants filter compatible with genome browser location strings
  • Support for custom public igv tracks stored on the cloud
  • Add tests to increase testing coverage
  • Update case variants count after deleting variants
  • Update IGV.js to latest (v2.7.4)
  • Bypass igv.js CORS check using https://github.com/Rob--W/cors-anywhere
  • Documentation on default and custom IGV.js tracks (admin docs)
  • Lock phenomodels so they're editable by admins only
  • Small case group assessment sharing
  • Tutorial and files for deploying app on containers (Kubernetes pods)
  • Canonical transcript and protein change of canonical transcript in exported variants excel sheet
  • Support for Font Awesome version 6
  • Submit to Beacon from case page sidebar
  • Hide dismissed variants in variants pages and variants export function
  • Systemd service files and instruction to deploy Scout using podman

Fixed

  • Bugfix: unused chromgraph_prefix |tojson removed
  • Freeze coloredlogs temporarily
  • Marrvel link
  • Don't show TP53 link for silent or synonymous changes
  • OMIM gene field accepts any custom number as OMIM gene
  • Fix Pytest single quote vs double quote string
  • Bug in gene variants search by similar cases and no similar case is found
  • Delete unused file userpanel.py
  • Primary transcripts in variant overview and general report
  • Google OAuth2 login setup in README file
  • Redirect to 'missing file'-icon if configured Chromograph file is missing
  • Javascript error in case page
  • Fix compound matching during variant loading for hg38
  • Cancer variants view containing variants dismissed with cancer-specific reasons
  • Zoom to SV variant length was missing IGV contig select
  • Tooltips on case page when case has no default gene panels

Changed

  • Save case variants count in case document and not in sessions
  • Style of gene panels multiselect on case page
  • Collapse/expand main HPO checkboxes in phenomodel preview
  • Replaced GQ (Genotype quality) with VAF (Variant allele frequency) in cancer variants GT table
  • Allow loading of cancer cases with no tumor_purity field
  • Truncate cDNA and protein changes in case report if longer than 20 characters
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