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Releases: EUCANCan/oncoliner

v1.1.1

05 Sep 13:03
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v1.1.1 (2024-09-05)

Fix

  • fix: Fix Docker compatibility (652dd3b)

v1.1.0

17 Jul 08:00
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v1.1.0 (2024-07-17)

Feature

Fix

  • fix(UI): Remove reference to old H_score (970e567)

  • fix(PipelineDesigner): Fix max-recommentions arg type (0883a91)

  • fix: Fix assessment typo (38bf0dc)

  • fix: Rename PHS and remove actionable genes (02e101b)

Performance

  • perf(Improvement): Optimize multi-core analysis (0aa662b)

v1.0.0

04 Dec 15:54
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v1.0.0 (2023-12-04)

Breaking

  • fix: Fix Dockerfile

BREAKING CHANGE: Dummy to trigger 1.0.0 (de5cfc0)

Feature

  • feat(UI): Prettify tables (b009917)

  • feat(UI): Prettify variant callers names (aeb8cf8)

  • feat(UI): Add harmonization text and style (c67d1c7)

  • feat(UI): Add style and text for improvement tab (738b3f7)

  • feat(UI): Add default column ordering (6f792fc)

  • feat: Add fixed row with the baseline (3907eab)

  • feat: Add variant callers combinations (4fbc459)

  • feat(Harmonization): Add heterogeneity scores (91c2907)

  • feat: Add VCF intersect and union tools (d4b9686)

  • feat(UI): Add text to improvement and harmonization (6dd652d)

  • feat: Add actionable genes (d87bcfe)

  • feat: Add prunning to harmonization (d34155b)

  • feat: Add PipelineDesigner prunning (e7224d4)

  • feat: Add improvement pruning (3611188)

  • feat: Rework pipeline designer to work with configuration files (1b871fd)

  • feat: Rework harmonizator (b36e0f9)

  • feat: Add variant types parameter for filtering (5e6ff2f)

Fix

  • fix(UI): Fix harmonization display (6501a55)

  • fix(UI): Selection in dropdown accordion now displays its hierarchy (#3)

Co-authored-by: Henri de Soyres <[email protected]> (23cea50)

  • fix(UI): Add clarifications for improvement and harmonization (59ab36c)

  • fix(UI): Fix loading screen not appearing (4c88a3a)

  • fix(UI): Remove callers folders parameter (b628991)

  • fix(UI): Hide callers in collapsable for improvement (efd2e8b)

  • fix: Remove variant callers combinations from repo (3489187)

  • fix(Assesment): Remove genes from stdout output (f9ea399)

  • fix(UI): Remove lateral panels in improvement and harmonization (#2)

  • removed left panel for improvement and harmonization views, changed into tab and new component: dropdown tree

  • replaced variant type and size dropdown menu from list to accordion tree


Co-authored-by: Henri de Soyres <[email protected]> (a2bc9f9)

  • fix(UI): Improve FP visibility in assesment (9b5c62b)

  • fix(Harmonizator): Fix misordering of pipelines recomendations (2ae66ab)

  • fix(UI): Remove genes from output tables (53bd5b5)

  • fix: Fix gene aggregation (a7dc290)

  • fix: Fix gene annotation I/O (e31f9e1)

  • fix: Fix missing "samples" subfolder in improvement (8d3c2a5)

  • fix: Fix missing baseline output in improvement (b5b7e64)

  • fix: Remove pandas deprecation warning (dbec680)

  • fix: Remove extra prints (52939bf)

  • fix: Fix VCFs with mixed chr and non-chr contigs (3d4371f)

  • fix: Improve input ingestion (5eef8bc)

Performance

  • perf(UI): Use default OS fonts (f7e0851)

  • perf(UI): Improve performance when generating report (d0e0228)

  • perf: Improve VCF intersection performance (3af5c5d)

Unknown

  • deps(UI): Change HTML minify library (8c67f1a)

v0.2.0

04 Dec 12:29
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v0.2.0 (2023-12-04)

Feature

  • feat(UI): Prettify tables (b009917)

  • feat(UI): Prettify variant callers names (aeb8cf8)

  • feat(UI): Add harmonization text and style (c67d1c7)

  • feat(UI): Add style and text for improvement tab (738b3f7)

  • feat(UI): Add default column ordering (6f792fc)

  • feat: Add fixed row with the baseline (3907eab)

  • feat: Add variant callers combinations (4fbc459)

  • feat(Harmonization): Add heterogeneity scores (91c2907)

  • feat: Add VCF intersect and union tools (d4b9686)

  • feat(UI): Add text to improvement and harmonization (6dd652d)

  • feat: Add actionable genes (d87bcfe)

  • feat: Add prunning to harmonization (d34155b)

  • feat: Add PipelineDesigner prunning (e7224d4)

  • feat: Add improvement pruning (3611188)

  • feat: Rework pipeline designer to work with configuration files (1b871fd)

  • feat: Rework harmonizator (b36e0f9)

  • feat: Add variant types parameter for filtering (5e6ff2f)

Fix

  • fix(UI): Fix harmonization display (6501a55)

  • fix(UI): Selection in dropdown accordion now displays its hierarchy (#3)

Co-authored-by: Henri de Soyres <[email protected]> (23cea50)

  • fix(UI): Add clarifications for improvement and harmonization (59ab36c)

  • fix(UI): Fix loading screen not appearing (4c88a3a)

  • fix(UI): Remove callers folders parameter (b628991)

  • fix(UI): Hide callers in collapsable for improvement (efd2e8b)

  • fix: Remove variant callers combinations from repo (3489187)

  • fix(Assesment): Remove genes from stdout output (f9ea399)

  • fix(UI): Remove lateral panels in improvement and harmonization (#2)

  • removed left panel for improvement and harmonization views, changed into tab and new component: dropdown tree

  • replaced variant type and size dropdown menu from list to accordion tree


Co-authored-by: Henri de Soyres <[email protected]> (a2bc9f9)

  • fix(UI): Improve FP visibility in assesment (9b5c62b)

  • fix(Harmonizator): Fix misordering of pipelines recomendations (2ae66ab)

  • fix(UI): Remove genes from output tables (53bd5b5)

  • fix: Fix gene aggregation (a7dc290)

  • fix: Fix gene annotation I/O (e31f9e1)

  • fix: Fix missing "samples" subfolder in improvement (8d3c2a5)

  • fix: Fix missing baseline output in improvement (b5b7e64)

  • fix: Remove pandas deprecation warning (dbec680)

  • fix: Remove extra prints (52939bf)

  • fix: Fix VCFs with mixed chr and non-chr contigs (3d4371f)

  • fix: Improve input ingestion (5eef8bc)

Performance

  • perf(UI): Use default OS fonts (f7e0851)

  • perf(UI): Improve performance when generating report (d0e0228)

  • perf: Improve VCF intersection performance (3af5c5d)

Unknown

  • deps(UI): Change HTML minify library (8c67f1a)

v0.1.0

17 Oct 10:05
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v0.1.0 (2023-10-17)

Feature

  • feat(PipelineDesigner): Check for combination improvement (03152ae)

  • feat: Include UI module (1df8532)

  • feat: Add example to improvement module (6d024f1)

  • feat: Add public data example (40cb24d)

  • feat: Complete pipeline designer (775caaa)

  • feat: Add pipeline designer tool (d17058d)

  • feat: Add Dockerfile and singularity.def (4f6d8c6)

  • feat: Add improvement and harmonization (26c2418)

  • feat: Include assesment module (08090f2)

  • feat: Add harmonization and UI (7b7623a)

  • feat: Integrate with evaluation module (4876ebb)

Fix

  • fix: Add vcf_ops command tools (99972af)

  • fix: Update Docker and Singularity recipies (59deac9)

  • fix(UI): Change minification packages (683e3fa)

  • fix(UI): Add missing columns (a3731df)

  • fix(UI): Remove empty warnings (6ea051d)

  • fix: Change to window_radius in harmonization (45e28fb)

  • fix: Fix container files (20f8497)

  • fix: Remove deprecated .warn (07742e4)

  • fix: Change to warning if pipeline folder has more samples than config (567d042)