Version 1.6.1

• Change 'reads' to 'sites' in PWGS plot label and round cutoff up to nearest integer

What's Changed

• Release 1.6.1 by @iainrb in #400

Full Changelog: v1.6.0...v1.6.1

Version 1.6.0

What's Changed

• Release 1.6.0 by @iainrb in #399
  Full Changelog: v1.5.6...v1.6.0

New features

• Support for WGS 4.0 assay
• Purple CNV plugin
• Added LOH and HRD to clinical reports
• Support for plugins outwith the main Djerba repository

Version 1.6.0-gamma

Summary

Final testing for the 1.6.0 release

What's Changed

• WGS assay 4.0 draft by @iainrb in #366
• Replace input_params_tools with read_maybe_input_params in workspace by @iainrb in #367
• Update all curated gene list for oncoKB by @OumaimaHamza in #368
• Fix gcgi 1317 write purple copy states by @iainrb in #369
• Fix gcgi 1320 cnv dependency by @iainrb in #370
• Update genomic landscape to read purity from PURPLE output by @iainrb in #371
• LOH Addition! by @AqsaAlam in #372
• Dev gcgi 993 multiple plugin packages by @iainrb in #373
• Bug fix metrix cell by @AqsaAlam in #375
• Support PWGS in mini-Djerba by making summary optional by @iainrb in #376
• Warning instead of error on inconsistent sample names by @iainrb in #377
• Added ARID2 to swi snf gene list by @AqsaAlam in #378
• Fix case_overview config by @iainrb in #381
• Fix remove copy state by @AqsaAlam in #382
• Remove obsolete provenance_tools from genomic_landscape by @iainrb in #384
• Import the traceback module in core.render by @iainrb in #383
• GCGI-1318, pWGS report improvements by @OumaimaHamza in #374
• pWGS formatting fixes by @OumaimaHamza in #385
• Add loh to disclaimer by @AqsaAlam in #386
• Write updated JSON by default, with a more informative name by @iainrb in #387
• Dev gcgi 1344 checksum fix by @iainrb in #388
• Update checksums; tests on 1.6.0 release branch now pass by @iainrb in #389
• Update plugin lists for djerba.py setup mode by @AqsaAlam in #390
• Fix gcgi 1348 benchmark tests by @iainrb in #391
• Adjusting pWGS e-signature spacing by @OumaimaHamza in #392
• Merge changes from release v1.5.6 and fix conflicts by @iainrb in #396

New Contributors

• @OumaimaHamza made their first contribution in #368

Full Changelog: v1.5.6...v1.6.0-gamma

Version 1.5.6

• Fix to TERT protein annotation (G>A -> C>T)
• Removed extra white space in gene information section

Version 1.6.0-beta

Summary

Pre-release to apply fixes to pWGS report generation

What's Changed

• WGS assay 4.0 draft by @iainrb in #366
• Replace input_params_tools with read_maybe_input_params in workspace by @iainrb in #367
• Update all curated gene list for oncoKB by @OumaimaHamza in #368
• Fix gcgi 1317 write purple copy states by @iainrb in #369
• Fix gcgi 1320 cnv dependency by @iainrb in #370
• Update genomic landscape to read purity from PURPLE output by @iainrb in #371
• LOH Addition! by @AqsaAlam in #372
• Dev gcgi 993 multiple plugin packages by @iainrb in #373
• Bug fix metrix cell by @AqsaAlam in #375
• Support PWGS in mini-Djerba by making summary optional by @iainrb in #376
• Warning instead of error on inconsistent sample names by @iainrb in #377
• Added ARID2 to swi snf gene list by @AqsaAlam in #378
• Fix case_overview config by @iainrb in #381
• Fix remove copy state by @AqsaAlam in #382
• Remove obsolete provenance_tools from genomic_landscape by @iainrb in #384
• Import the traceback module in core.render by @iainrb in #383
• GCGI-1318, pWGS report improvements by @OumaimaHamza in #374
• pWGS formatting fixes by @OumaimaHamza in #385

New Contributors

• @OumaimaHamza made their first contribution in #368

Full Changelog: v1.5.5...v1.6.0-beta

Version 1.6.0-alpha

Alpha release of 1.6.0 for evaluation and testing

What's Changed

• WGS assay 4.0 draft by @iainrb in #366
• Replace input_params_tools with read_maybe_input_params in workspace by @iainrb in #367
• Update all curated gene list for oncoKB by @OumaimaHamza in #368
• Fix gcgi 1317 write purple copy states by @iainrb in #369
• Fix gcgi 1320 cnv dependency by @iainrb in #370
• Update genomic landscape to read purity from PURPLE output by @iainrb in #371
• LOH Addition! by @AqsaAlam in #372
• Dev gcgi 993 multiple plugin packages by @iainrb in #373

New Contributors

• @OumaimaHamza made their first contribution in #368

Full Changelog: v1.5.5...v1.6.0-alpha

Version 1.5.5

• Further fixes to pWGS Cardea helper to allow multiple projects for one donor

Version 1.5 4

• Fixed pWGS Cardea helper, pWGS provenance helper

Version 1.5.3

• GCGI-1280: Allow wgts.snv_indel plugin to run as standalone
• Enable fallback values when updating null parameters from JSON

What's Changed

• Dev gcgi 1280 snv indel standalone by @iainrb in #359

Full Changelog: v1.5.2...v1.5.3

Version 1.5.2

Minor fixes to benchmarking

• GCGI-1299: Redact gene descriptions in benchmark comparison
• GCGI-1301: Add report title and patient info to benchmark INI