v1.8.0-rc3

What's Changed

• Adds the functionality to convert gtc-to-bcf. by @rajwanir in #346
• fix: Unexpected replicate count incorrect when group of 3 or more (issue #352) by @jaamarks in #355
• report: Remove the sentence about low replicate concordance (issue #353) by @jaamarks in #354
• fix: .nosex missing issue (Issue 349) by @carynwillis in #356

Full Changelog: v1.7.0...v1.8.0-rc3

v1.8.0-rc2

What's Changed

• fix: Unexpected replicate count incorrect when group of 3 or more (issue #352) by @jaamarks in #355
• report: Remove the sentence about low replicate concordance (issue #353) by @jaamarks in #354

Full Changelog: v1.8.0-rc1...v1.8.0-rc2

v1.8.0-rc1

What's Changed

• Adds the functionality to convert gtc-to-bcf. by @rajwanir in #346

Full Changelog: v1.7.0...v1.8.0-rc1

v1.7.0

What's Changed

• feat: Add data dictionary for QC_Report to delivery folder (issue #313) by @jaamarks in #317
• fix: Handle removal of discordant expected replicates (issue #210) by @jaamarks in #319
• report: Clarify loci filter precedence in QC_Report.docx (issue #288) by @jaamarks in #320
• feat: Improve handling of unexpected replicates (issue #269) by @jaamarks in #322
• feat: BCF entry point with intensity and contamination checks using BCF for data_catalog usage. by @rajwanir in #314
• fix: Convert missing ancestry to Other category for grafpop output (issue #326) by @carynwillis in #331
• fix: Handling Chr Y saps and revert to GTC to PED (issue #308) by @carynwillis in #332
• feat: Improve handling of discordant expected replicates (issue #324) by @jaamarks in #327
• depends: Upgrade Black, Typer, etc (issue #323) by @jaamarks in #325
• fix: Handle cases when contamination=<NA> (issue #269) by @jaamarks in #333
• feat: add max_time_hr option for wall-time allocation (issue #334) by @jaamarks in #335
• test: Add skipif decorator to handle CGEMS directory access (issue #336) by @jaamarks in #337
• fix: Apply max_time_hr to sample_level_ibd rule (issue #334) by @jaamarks in #342
• feat: Add max_mem_mb config option to set max memory available (issue #343) by @jaamarks in #344
• fix: cleaner data handling and improved logic for sample_qc_table.py (issue #324) by @jaamarks in #345

New Contributors

• @rajwanir made their first contribution in #314

Full Changelog: v1.6.0...v1.7.0

v1.7.0-rc1

What's Changed

expand

• feat: Add data dictionary for QC_Report to delivery folder (issue #313) by @jaamarks in #317
• bugfix: Handle removal of discordant expected replicates (issue #210) by @jaamarks in #319
• report: Clarify loci filter precedence in QC_Report.docx (issue #288) by @jaamarks in #320
• feat: Improve handling of unexpected replicates (issue #269) by @jaamarks in #322
• BCF entry point with intensity and contamination checks using BCF for data_catalog usage. by @rajwanir in #314
• bugfix: Convert missing ancestry to Other category for grafpop output (Issue 326) by @carynwillis in #331
• BugFix: Handling Chr Y saps and revert to GTC to PED (Issue 308) by @carynwillis in #332
• feat: Improve handling of discordant expected replicates (issue #324) by @jaamarks in #327
• dependencies: Upgrade Black, Typer, etc (issue #323) by @jaamarks in #325
• bugfix: Handle cases when contamination=<NA> (issue #269) by @jaamarks in #333
• feat: add max_time_hr option for wall-time allocation (issue #334) by @jaamarks in #335
• test: Add skipif decorator to handle CGEMS directory access (issue #336) by @jaamarks in #337
• bugfix: Apply max_time_hr to sample_level_ibd rule (issue #334) by @jaamarks in #342
• feat: Add max_mem_mb config option to set max memory available (issue #343) by @jaamarks in #344
• bugfix: cleaner data handling and improved logic for sample_qc_table.py (issue #324) by @jaamarks in #345

New Contributors

• @rajwanir made their first contribution in #314

Full Changelog: v1.6.0...v1.7.0-rc1

v1.6.0

What's Changed

• 287 dynamically adjust minimum maf for hwe calculation and add option to set hwe p value threshold by @kliao12 in #300
• fix checkpoint to check populations for # controls by @kliao12 in #301
• switch snp and call rate filters by @kliao12 in #305
• bugfix: is_unexpected_replicate data missing in QC_Report.xlsx by @jaamarks in #304
• bugfix: retrieve additional missing data from QC_Report.xlsx by @jaamarks in #307
• gtc to ped (Issue 222) by @carynwillis in #309
• Update branch by @kliao12 in #311
• 302 skip merging graf king and plink results to make the qc pipeline more efficient by @kliao12 in #310

Full Changelog: v1.5.1...v1.6.0

v1.5.1

What's Changed

• 281 ancestry = unknown not shown in table 3 subject counts by ancestry group by @kliao12 in #290
• bugfix: error when setting case_control_gwas=true by @jaamarks in #291
• refactor: update python deploy workflow by @jaamarks in #298
• performance: improve memory allocation for sample_qc subworkflow by @jaamarks in #299
• performance: more aggressive time scaling in sample_qc by @jaamarks in #297

Full Changelog: v1.5.0...v1.5.1

v1.5.0

What's Changed

• Fix documentation auto implementation of version release by @kliao12 in #278
• Update readme by @kliao12 in #279
• feature: add a generic slurm cluster submit option by @jaamarks in #283
• fix empty relatedness files by @kliao12 in #284
• add pulp2.7.0 to pyproject.toml by @kliao12 in #286

Full Changelog: v1.4.0...v1.5.0

v1.4.0

What's Changed

• Lims upload formatting by @carynwillis in #266
• Fixes #240: convert alt case/control labels to Unknown by @jaamarks in #267
• sort IBD and Family tabs in QC_Report by @carynwillis in #270
• Fix memory issues for larger sample sizes by @jaamarks in #271
• Refactor to capture exit_status for successful runs by @jaamarks in #272
• Issue 237 by @kliao12 in #274
• Automatic Lims upload capability and QC table column additions by @carynwillis in #275
• Correct column names for testing by @carynwillis in #276
• Correct column name for analytic_exclusion by @carynwillis in #277

New Contributors

• @carynwillis made their first contribution in #266
• @jaamarks made their first contribution in #267

Full Changelog: v1.3.0...v1.4.0

v1.3.0

This release implements graf2.4 and grafpop into the pipeline. grafpop is an updated method used for ancestry inference that utilizes more SNPs compared to the old graf. Processing of graf output into downstream reports were also implemented.

What's Changed

• Pull updates from default by @jsanjak in #255
• Update README.md by @jsanjak in #256
• Dev/sphinx success by @jsanjak in #257
• Pull from default by @jsanjak in #258
• Dev/dev docs by @jsanjak in #260
• Grafpop and graf2.4 implementation by @kliao12 in #263

Full Changelog: v1.2.0...v1.3.0