v1.0

What's Changed

• AXIN hotfix by @kachulis in #169
• Fixed error in CreateAggregationSets when reading booleans as strings by @michaelgatzen in #171
• Hotfix: Update IGV xml writing docker to get benchmark tests passing by @kachulis in #172
• Glimpse/htslib retries & bug fix, and index specification by @kachulis in #173
• Keep stderr consistent for OOM checks in Glimpse pipeline by @kachulis in #174
• Use watt for tests by @kachulis in #176
• Fix version parsing errors when building with pip by @kachulis in #175
• PRSQC WDL First Iteration by @kockan in #177
• Adding Glimpse2ImputationAndCheckQC wrapper WDL by @michaelgatzen in #180
• Made changes to the output files/formats for compatibility with the d… by @kockan in #181
• Testing overhaul by @kachulis in #179
• PRS Scoring Pipeline for BGE by @michaelgatzen in #178
• Test only WDLs with changed dependencies by @kachulis in #186
• Fix for ScoreBGE by @michaelgatzen in #187
• Glimpse tests by @kachulis in #183
• The Big Benchmarking PR by @rickymagner in #167
• Update various PRS related tasks with plink chromosome encodings by @kachulis in #189
• Fix whitespace in some recent changes by @rickymagner in #190
• Improvements to ScoreBGE and LiftoverSites by @michaelgatzen in #193
• Modifications (in progress) to the PRSQC workflow to fit the OC input… by @kockan in #195
• cBGE output format changes by @michaelgatzen in #194
• Scatter Glimpse Merge by @kachulis in #188
• Exposed PRSQC distance_threshold to PCAREAndQC by @michaelgatzen in #197
• Exposed imputed_vcf_md5sum output to Glimpse2ImputationAndCheckQC by @michaelgatzen in #198
• fix Glimpse2MergeBatches.MergeQCMetrics by @kachulis in #200
• Update BenchmarkSVs workflow(s) with some new features by @rickymagner in #199
• Python testing and linting by @kachulis in #191
• Dockerfile tests and cleanup imputation/PRS by @kachulis in #202
• Fix PRS validation wdl by @kachulis in #204
• GLIMPSE2 improvements by @michaelgatzen in #203
• Update vcfeval docker image by @rickymagner in #182
• more ImputationPipeline --> PRS by @kachulis in #205
• Wire Glimpse phasing runtime params into outer workflow by @geoffjentry in #207
• BGE gCNV by @kachulis in #206
• Fix and improve panel count calculation in gcnv filtering by @kachulis in #208
• Always generate merged vcf, regardless of cnv qc status by @kachulis in #209
• Move tests to GCPBatch by @kachulis in #212
• Add final files: EBMs notebook and pipeline.wdl by @Eyad-Alqaysi in #185
• Optimize cnv wdl for single sample by @kachulis in #211
• MergeSingleSampleMinimacVcfs by @kachulis in #201
• Add gCNV event visualization report by @kachulis in #210
• Expose memory parameter in GCNVVisualization by @kachulis in #215
• CNV Control Events QC by @michaelgatzen in #216
• Expose parameters, remove unused tasks by @kachulis in #219
• Bump cromwell version to 89 for tests by @kachulis in #220
• Fix Python-Data-Slim Dockerfile by @kachulis in #221
• Add trio analysis workflow by @rickymagner in #218
• Add AnnotateVCF pipeline and refactor by @rickymagner in #214
• Added CleanSVs.wdl to dockstore.yml by @kockan in #223
• Automate export for Glimpse2SplitReference by @michaelgatzen in #213
• BGESexEstimation script by @michaelgatzen in #224
• CNVControlEventsQC: Fix crash if eval VCF has no passing events by @michaelgatzen in #225
• Glimpse QC report (improved) by @kachulis in #226

Full Changelog: v0.17...v1.0