Version 1.7.9

Highlights

• Updated contact name/address on report letterhead
• Overhaul of GSICAPBENCH evaluation, with support for TAR and PWGS
• Remove "failed report " plugin, transfer functionality to "summary" plugin
• Remove the Sequenza CNV plugin
• Updated total genome segment length constant in percent genome altered calculation

What's Changed

• Dev gcgi 1378 new gsicapbench inputs by @iainrb in #486
• Update 1.7.8 with latest changes from main by @iainrb in #492
• Add new JSON diff script and tests by @iainrb in #493
• Gcgi 1472 grab all patient ids by @AqsaAlam in #495
• Allowed tumour and normal ids to be manually specified for provenance helper by @AqsaAlam in #496
• Added oncokb definitions to 40x assays by @AqsaAlam in #497
• Dev-GCGI-1446_fusion-total by @OumaimaHamza in #498
• self.patient_id_raw defaults to None when not in use by @iainrb in #499
• Dev gcgi 1326 whizbam links for fusions by @OumaimaHamza in #487
• Release 1.7.8 update by @OumaimaHamza in #500
• Fusion plugin test fixup by @iainrb in #501
• Fix arguments in calls to get_logger by @iainrb in #503
• Dev gcgi 1478 more informative logger name by @iainrb in #505
• Add --pre-populate option by @iainrb in #506
• Dev gcgi 1481 raw coverage autofill by @OumaimaHamza in #504
• Gcgi 1480 email in header by @AqsaAlam in #508
• Remove the Sequenza CNV plugin by @iainrb in #510
• Remove input paths from pwgs.analysis results by @iainrb in #511
• Gcgi 1413 move failed report plugin to summary by @AqsaAlam in #489
• Support TAR and PWGS in GSICAPBENCH by @iainrb in #509
• Release 1.7.9 by @iainrb in #512

Full Changelog: v1.7.8...v1.7.9

Version 1.8.0-beta

Merge changes from release 1.7.8 and fix conflicts

What's Changed

• Release 1.7.8 by @OumaimaHamza in #502

Full Changelog: v1.8.0-alpha...v1.8.0-beta

v1.7.8

Summary

• Standalone script for comparing two Djerba JSON reports.
• OncoKB enhancements: Added definitions to WGTS40X and WGS40X assays.
• Provenance improvements: Prevents overwriting manually provided tumor and normal IDs.
• Case Overview updates: Includes all patient IDs, not just the initial ID.
• Fusion viewing: Whizbam links for split-view visualization of fusions.

What's Changed

• Added standalone diff script for Djerba JSON reports by @iainrb in #493
• Included OncoKB definitions for WGTS40X and WGS40X assays by @AqsaAlam in #497
• Prevented manual ID overwrites in provenance_helper by @AqsaAlam in #496
• Updated case_overview to show all patient IDs by @AqsaAlam in #495
• Generated whizbam split-view fusion links by @OumaimaHamza in #487
• Release 1.7.8 by @OumaimaHamza in #502

Full Changelog: v1.7.7...v1.7.8

Version 1.8.0-alpha

• alpha release for evaluation and testing of replacing R scripts with Python
• Incorporates recent changes from the release-1.7.8 branch
• This and subsequent pre-releases of 1.8.0 will be tagged on the release-1.8.0 branch

What's Changed

• Dev gcgi 1378 new gsicapbench inputs by @iainrb in #486
• Update 1.7.8 with latest changes from main by @iainrb in #492
• Add new JSON diff script and tests by @iainrb in #493
• Dev mcgill r2python by @MareikeJaniak in #460
• Gcgi 1472 grab all patient ids by @AqsaAlam in #495
• Allowed tumour and normal ids to be manually specified for provenance helper by @AqsaAlam in #496
• Added oncokb definitions to 40x assays by @AqsaAlam in #497
• Dev-GCGI-1446_fusion-total by @OumaimaHamza in #498
• Dev mcgill purple by @MareikeJaniak in #476

New Contributors

• @MareikeJaniak made their first contribution in #460

Full Changelog: v1.7.7...v1.8.0-alpha

Version 1.7.7

Summary

• New virus plugin, for research use only
• Fixes to OncoKB cache
• Make study required in PWGS
• Make default geneticist sign-off data a "yyyy-mm-dd" placeholder

What's Changed

• Dev gcgi 1437 oncokb cache checking by @iainrb in #482
• Fix gcgi 1424 non latin cache by @iainrb in #483
• Gcgi 1460 make study required pwgs by @AqsaAlam in #484
• Changed geneticist sign off to yyyy-mm-dd and updated CHANGELOG by @AqsaAlam in #485
• Dev virus plugin by @AqsaAlam in #444
• Fix gcgi 1465 incorrect date check by @iainrb in #490
• Release 1.7.7 by @iainrb in #491

Full Changelog: v1.7.6...v1.7.7

Version 1.7.6

What's Changed

• GCGI-1156: Merge long-running documentation branch to main
• GCGI-1452: Update disclaimer with somatic mutation text and laboratory disclaimer
• GCGI-1453: Update pWGS version number
• GCGI-1456: Fix rounding of estimated tumour fraction in tar.sample
• Increase csv field limit in plugins.fusions.tools.py to handle large fields in mavis_summary.txt
• Bold HRD definition

Version 1.7.5

What's Changed

• GCGI-1378 gsicapbench update by @iainrb in #469
• Type error before inner join by @OumaimaHamza in #470
• Gcgi 1477 key error copy state by @AqsaAlam in #471
• Release 1.7.5 by @iainrb in #472

Full Changelog: v1.7.4...v1.7.5

Version 1.7.4

What's Changed

• Fix GCGI-1442 N4 fusion annotation by @iainrb in #465
• Skip 'NA' values for 'seg.mean' in fraction genome altered by @iainrb in #466
• Fix for inconsistent MD5 of gzip output in provenance helper test by @iainrb in #467
• Release 1.7.4 by @iainrb in #468

Full Changelog: v1.7.3...v1.7.4

v1.7.3

Highlights

• HRD can handle unknown oncotree codes
• Updates to targeted panel
• Placeholder text for clinical geneticist name and ID

Details

• GCGI-1438: Updated genomic landscape plugin (hrd.py) to handle unknown oncotree codes for treatment options
• GCGI-1262: Remove ABCB1 from TAR reports
• Add CDH1, NF1, and VHL to new targeted panel (v2.0 -> v3.0)
• GCGI-1333/1441: Make TAR depend on provenance helper
• GCGI_1439: Changed clinical geneticist's name and number to PLACEHOLDER and XXXXXXX respectively

Full Changelog: v1.7.2...v1.7.3

Version 1.7.2

What's changed

• GCGI-1420: Added green line separator to research footer
• GCGI-1419: Fixed callability fetching in sample plugin to use donor as well as tumour_id