v13.2.0

What's Changed

• assay information was being incorrectly processed by @thomasyu888 in #457
• [IBCSPRT-35] Add clinicalReported column to genomic information file by @thomasyu888 in #459
• [ETL-156, ETL-157, ETL-158] Create configuration dictionary for GENIE code by @thomasyu888 in #455

Full Changelog: v13.1.0...v13.2.0

v13.1.1

What's Changed

• assay information was being incorrectly processed by @thomasyu888 in #457

Full Changelog: v13.1.0...v13.1.1

v13.1.0

What's Changed

• Update pandas version by @thomasyu888 in #446
• Release v13.0.0 by @thomasyu888 in #447
• Add code of conduct by @thomasyu888 in #448
• year or int of death is not applicable for living patients by @hhunterzinck in #450
• support scheduled job secrets by @thomasyu888 in #453

New Contributors

• @hhunterzinck made their first contribution in #437

Full Changelog: v13.0.0...v13.1.0

v13.0.0

What's Changed

• Release 12.7.0 by @thomasyu888 in #425
• Add in codeowners for auto reviewers by @thomasyu888 in #428
• Fix installation for python packages by @thomasyu888 in #430
• Don't cache local install by @thomasyu888 in #431
• Revise dashboards by @thomasyu888 in #433
• fixes to seq-assay-id validation checks by @hhunterzinck in #437
• Modify tsa1, tsa2, ref maf error message by @thomasyu888 in #438
• Add sample class filter by @thomasyu888 in #441
• Fix Docker build by @thomasyu888 in #445

New Contributors

• @hhunterzinck made their first contribution in #437

Full Changelog: v12.7.0...v13.0.0

v12.7.0

What's Changed

• Make consortium releases = public releases, add dashboard plots/tables by @thomasyu888 in #385
• Add 'Not released' value by @thomasyu888 in #389
• Calculate missing counts by @thomasyu888 in #388
• Fix docker by @thomasyu888 in #396
• check for vital status inconsistencies by @thomasyu888 in #416
• Update Dockerfile by @thomasyu888 in #417
• Use new rsa decryption by @thomasyu888 in #419
• Some sites submitted csv files with completely empty rows by @thomasyu888 in #420
• No need to have different data guides for the public dataset anylonger by @thomasyu888 in #422
• Run black the python autoformatter on all files except for test files by @thomasyu888 in #421
• Add contributing guide by @thomasyu888 in #423
• Update CI/CD by @thomasyu888 in #424
• numpy array doesn't have .isin attribute by @thomasyu888 in #427

Full Changelog: v12.6.0...v12.7.0

v12.6.0

What's Changed

• Make sure new dashboard files aren't copied as a public file by @thomasyu888 in #401
• Turn all values to str by @thomasyu888 in #403
• Must support when bed file starts with X or Y by @thomasyu888 in #404
• Add missing assay info to dashboard by @thomasyu888 in #405
• Add chardet to requirements by @thomasyu888 in #406
• Add SAMPLE_CLASS, remove unnecessary clinical code by @thomasyu888 in #407
• Only query successful annotations by @thomasyu888 in #411
• Fix mergecheck - only query successfully annotated mutations by @thomasyu888 in #413
• Check for missing seq assay id in the assay information file by @thomasyu888 in #415
• Release v12.6.0 by @thomasyu888 in #418

Full Changelog: v12.5.0...v12.6.0

v12.5.0

GENIE releases:

• 10.3-consortium
• 10.4-consortium
• 10.5-consortium
• 10.6-consortium
• 10.0-public
• 11.1-consortium
• 11.2-consortium
• 11.3-consortium
• 11.4-consortium
• 11.5-consortium
• 11.6-consortium
• 11.0-public

Changelog:

• Implement whitelisted variants by pulling from known somatic sites
• Update Dockerfile

What's Changed

• Hotfix by @thomasyu888 in #399
• Update version by @thomasyu888 in #400

Full Changelog: v12.4.0...v12.5.0

v12.4.0

GENIE releases:

• 10.2-consortium

Changelog:

• Make consortium releases = public releases, add dashboard plots/tables
• Fix Dockerfile

What's Changed

• HTML links need to open in new tab in dashboard html by @thomasyu888 in #392
• Add novaseq panel by @thomasyu888 in #394
• Fix dashboard table updater by @thomasyu888 in #395
• Release 12.4.0 by @thomasyu888 in #398

Full Changelog: v12.3.0...v12.4.0

v12.3.0

GENIE releases:

• 10.1-consortium

Changelog:

• Add to dashboard html
• Don't release NULL oncotree codes to consortium release
• Add 'Not Released' to vital status
• Fill missing variant counts

What's Changed

• VCF validation doesn't need ID column by @thomasyu888 in #379
• Strip white space from str columns prior to checking duplicated variant by @thomasyu888 in #380
• Add MAF file validation - numerical columns must be numerical by @thomasyu888 in #386
• Release v12.3.0 by @thomasyu888 in #391

Full Changelog: v12.2.0...v12.3.0

v12.2.0

GENIE releases:

• 9.6-consortium
• 9.0-public

Changelog:

• Add provenance to tables and release files
• Update synapseclient
• Remove ascii characters from data guide template
• add public data guide template until I can figure out how to add logic into the templates
• Don't copy samples_to_retract.csv
• Reorder maf file because it seems genome nexus returns maf files in different column orders now.
• Fix paths to templates and R
• Create case lists with assay_information.txt
• Make sure there are no null gene symbols in fusion file.