v2.8.5

What's Changed

• TASK-2254 - Error processing job output - malformed VCF and disk quota exceeded by @pfurio in #2352
• TASK-5166 - The CLI upload service does not display error messages. by @juanfeSanahuja in #2355

Full Changelog: v2.8.4...v2.8.5

v2.8.4

What's Changed

• TASK-4913 - Unable to update cellbase-token by @j-coll in #2329
• TASK-4688 - Avoid git.properties collision by @j-coll in #2335
• TASK-5027 - NullPointerException executing JUnit tests SampleIndexOnlyVariantQueryExecutor by @j-coll in #2340
• TASK-4938 - OpenCGA VariantExport tests sometimes throw a ConcurrentModificationException by @j-coll in #2338
• TASK-4945 - OpenCGA Status not being updated by @j-coll in #2339
• TASK-4853 - OutOfMemoryError running CatalogStorageMetadataSynchronizer by @j-coll in #2324
• TASK-4843 - CLI Fails uploading file by @juanfeSanahuja in #2323
• TASK-4210 - Catalog delete operations may not check if data is used in Clinical Analyses by @pfurio in #2343
• TASK-5038 - Update signature.tools.lib package to fix fitting and HRDetect analysis by @jtarraga in #2346
• TASK-4684 - AggregateFamily overwrites multiallelic information by @j-coll in #2321
• TASK-5083 - Sample - Case junit test not working by @pfurio in #2347
• TASK-4872 - NullPointerException at variant-secondary-sample-index by @j-coll in #2342
• TASK-4873 - Unable to update CellBase version by @j-coll in #2344
• TASK-4770 - Error running migration calculate_pedigree_graph by @jtarraga in #2314
• TASK-4889 - Broken custom commands in CLI by @j-coll in #2348
• TASK-5092 - The CICD to delete docker on merge fails by @juanfeSanahuja in #2349
• TASK-4899 - Abnormally slow variant-index postLoad for files with thousands of samples by @j-coll in #2345
• TASK-5092 - The CICD to delete docker on merge fails by @juanfeSanahuja in #2351

Full Changelog: v2.8.3...v2.8.4

v2.11.0

What's Changed

• TASK-4802 - Port Patch 2.8.2.1 -> 2.8.3 (XB 1.6.3.1 -> XB 1.6.4) by @juanfeSanahuja in #2315
• TASK-4712 - Include not working in project search by @pfurio in #2312
• TASK-4445 - Opencga long test fails by @j-coll in #2293
• TASK-4794 - Missing "FILTER" field in VCF generated (export step) while running Exomiser by @j-coll in #2318
• TASK-4816 - Error fetching original call for INDELs export step from exomiser from complex contigs by @j-coll in #2317
• TASK-4851 - Some Catalog tests are failing - Project include issue by @pfurio in #2322
• TASK-4810 - Port Patch 2.9.2 -> 2.11.0 (XB 1.7.2 -> 1.9.0) by @juanfeSanahuja in #2320
• TASK-4848 - Modifications related to pharmacogenomics causes test failures by @j-coll in #2326
• TASK-4917 - Error generating opencga clients by @pfurio in #2332
• TASK-4913 - Unable to update cellbase-token by @j-coll in #2331
• TASK-4248 - improve usage documentation of REST search endpoint by adding regexp comment by @pfurio in #2327
• TASK-4875 - Port Patch 2.8.4 -> 2.11.0 (XB 1.6.4 -> 1.9.0) by @juanfeSanahuja in #2334
• TASK-4641- Update according to CellBase changes and remove and use VersionUtils from java-common-libs by @jtarraga in #2328
• TASK-4372 - Hadoop ExportSnapshot by @j-coll in #2333
• TASK-4688 - Avoid git.properties collision by @j-coll in #2336

Full Changelog: v2.10.0...v2.11.0

v2.8.3

What's Changed

• TASK-4802 - Port Patch 2.8.2.1 -> 2.8.3 (XB 1.6.3.1 -> XB 1.6.4) by @juanfeSanahuja in #2315
• TASK-4712 - Include not working in project search by @pfurio in #2312
• TASK-4445 - Opencga long test fails by @j-coll in #2293
• TASK-4794 - Missing "FILTER" field in VCF generated (export step) while running Exomiser by @j-coll in #2318
• TASK-4816 - Error fetching original call for INDELs export step from exomiser from complex contigs by @j-coll in #2317
• TASK-4851 - Some Catalog tests are failing - Project include issue by @pfurio in #2322

Full Changelog: v2.8.2.1...v2.8.3

v2.9.2

Full Changelog: v2.9.1...v2.9.2

v2.10.0

What's Changed

• TASK-4289 - Upgrade JVM to 8u372 in opencga Docker by @imedina in #2296
• TASK-4464 - CI/CD - Migrate some test functionality from OpenCB to Xetabase and centralize the regression testing and reporting on it by @juanfeSanahuja in #2304
• TASK-4428 - Ability to handle Ext-Tools for OpenCGA by @imedina in #2303
• TASK-4593 HRDetect analysis not working with the current R library by @jtarraga in #2308
• TASK-4144 Fix structural variation (SV) catalogue counting in signature analysis by @jtarraga in #2310
• TASK-4686 Fix the analysis of pedigree graphs when running with multiple disorders that have ids/names containing multiple words by @jtarraga in #2309
• TASK-4146 - Filtering by gene/region not working for CNVs in sample variant browser by @j-coll in #2307
• TASK-4642 - Incorrect results when running Exomiser on INDELs and Multiallelic by @j-coll in #2306
• TASK-4736 - Error executing junit "VariantHadoopDBWriterTest.loadVariantsBasic" by @j-coll in #2311
• TASK-4667 - Port Patch 1.6.3.1 -> 1.8.0 by @juanfeSanahuja in #2313

Full Changelog: v2.9.1...v2.10.0

v2.8.2.1

What's Changed

• TASK-4593 HRDetect analysis not working with the current R library by @jtarraga in #2308
• TASK-4144 Fix structural variation (SV) catalogue counting in signature analysis by @jtarraga in #2310
• TASK-4686 Fix the analysis of pedigree graphs when running with multiple disorders that have ids/names containing multiple words by @jtarraga in #2309
• TASK-4146 - Filtering by gene/region not working for CNVs in sample variant browser by @j-coll in #2307
• TASK-4642 - Incorrect results when running Exomiser on INDELs and Multiallelic by @j-coll in #2306
• TASK-4736 - Error executing junit "VariantHadoopDBWriterTest.loadVariantsBasic" by @j-coll in #2311

Full Changelog: v2.8.2...v2.8.2.1

v2.9.1

What's Changed

• TASK-4430 - Error writing ExecutionResult in SMB by @j-coll in #2292
• TASK-4488 - Unable to run variant-export with storage.mode = read_only by @j-coll in #2294
• TASK-4406 - ISSUE Client wasn't released in the last versions by @juanfeSanahuja in #2289
• TASK-4450 - Exomiser details tab in the Sample Variant Browser doesn't show the results from Exomiser by @jtarraga in #2295
• TASK-3964 - ERROR 504 (42703): Undefined column - on variant query after file delete by @j-coll in #2297

Full Changelog: v2.9.0...v2.9.1

v2.8.2

What's Changed

• TASK-4430 - Error writing ExecutionResult in SMB by @j-coll in #2292
• TASK-4488 - Unable to run variant-export with storage.mode = read_only by @j-coll in #2294
• TASK-4406 - ISSUE Client wasn't released in the last versions by @juanfeSanahuja in #2289
• TASK-4450 - Exomiser details tab in the Sample Variant Browser doesn't show the results from Exomiser by @jtarraga in #2295
• TASK-3964 - ERROR 504 (42703): Undefined column - on variant query after file delete by @j-coll in #2297

Full Changelog: v2.8.1...v2.8.2

v2.9.0

What's Changed

• TASK-4163 - Modify build workflow to check the same branch name of dependency by @juanfeSanahuja in #2273
• TASK-4099 - Deprecate opencga-init container by @j-coll in #2290
• TASK-4157 - Implement support for setting a default data release for each CellBase version by @j-coll in #2288
• TASK-4364 - Add new administrator method to update user to synced groups by @pfurio in #2291

Full Changelog: v2.8.1...v2.9.0