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

v0.17

What's Changed

• Add pipelines for benchmarking and cleaning SV VCFs by @rickymagner in #159
• Update IntervalList2Bed to handle case of compressed interval file inputs by @rickymagner in #163
• Update CleanSVs and some typos in BenchmarkSVs by @rickymagner in #162
• Implement FindSamplesAndBenchmark wrapper for SimpleBenchmark by @rickymagner in #164
• Update dashboards to use quickboard v0.4.0 by @rickymagner in #165
• Add Checkpointing and QC Collection to GlimpseImputation by @michaelgatzen in #161

Full Changelog: v0.16...v0.17

v0.16

What's Changed

• Added a pipeline for phasing VCFs and benchmarking their performance with WhatsHap (#124)
• New Utilities WDL: DownsampleAndCollectCoverage (#132)
• Update .dockstore.yml to include Dipcall (#135)
• Update for PRS on hg38 (#137)
• New workflow: CompareBenchmarks and fixed repo CircleCI (#103)
• Add combine summaries wf (#112)
• Add error messages in R scripts rather than just quit for PRSWrapper (#141)
• Update RTG docker for vcfeval to fix FORMAT filters ignored (#142)
• vcfdist evaluation (#143)
• Toggle benchmark vc fs fingerprint (#144)
• Potential improvements regarding default thread numbers and disk sizes (#150)
• Handle ploidy in chrX and chrY outside of the PAR region for benchmarking (#133)
• Add utility for creating IGV session from list of bams, vcfs, intervals (#145)
• Add utility for converting interval_list to bed efficiently (#154)
• Rewrite SimpleBenchmark and merge for staging before replacing BenchmarkVCFs (#155)
• Add MatchFingerprints utility WDL (#156)
• Automatic Novelty Detection/Flagging from PCA plots (#157)
• Add CMRG interval files to our docs (#158)
• Add Glimpse2Imputation pipeline (#123)
• Pandas deprecated DataFrame.append in PRS QC (#160)

Full Changelog: v0.15...v0.16

v0.15

• Multiqc in Terra (#125)
• Added WDLs for the RNA QC metric collection/concordance as part of a (#127)
• Long Read RNA Benchmarking Pipeline First Draft (#126)
• BCFTools docker: Added the python-is-python3 package (#129)
• Added Dipcall WDL and reformat README for utilities (#130)
• PRS check z-score before APOL1 correction (#131)

Full Changelog: v0.14...v0.15

v0.14

BenchmarkVCFs

• SimpleBenchmark -- a new WDL for benchmarking VCFs (#115)

Utilities

• Added documentation on Interval Files commonly (#118)
• Added missing comma in interval list input for Terra (#119)
• Added utilities for bam stats over intervals (#120)
• Added pysam docker, for use elsewhere by (#121)

PRS

• AggregatePRSResults updates by (#122)

Full Changelog: v0.13...v0.14

v0.13

PRS

• Lowercase pcs in results csv (#117)

Full Changelog: v0.12...v0.13

v0.12

PRS

• Partial Aggregation Set handling, refactor, and testing(#114)
• Aggregate PCs, add tests (#116)

Full Changelog: v0.11...v0.12

v0.11

Utilities

• Updated CollectBenchmarkSucceeded utility (#109)

Functional Equivalence

• FE: rewrote F1 evaluation using Pandas by (#97)
• Updated python-data-slim and using it in FunctionalEquivalence WDLs (#111)

PRS

• QC Report updates by (#113)

Full Changelog: v0.10...v0.11

v0.10

Imputation/PRS

• Handle situation where control sample is not resulted for one conditions (#106)
• Improved formatting of samples table in prs aggregation report (#107)
• Automatically deliver QC'd results file to delivery bucket (#108)

v0.9

Imputation/PRS

• Handle no-calls at APOl1 risk alleles in ckd adjustment (#62)
• Added HTML report feature (#69)
• PRS Reportable Range Check (#88)
• Aggregate PRS Output (#92)
• Add Interaction terms to PRS pipeline (#90)
• Notebook for manual QC editing of prs results table (#93)
• PRS: Interactive PCA plot (#94)
• Changed batch_id to lab_batch and is_control to is_control_sample (#95)
• Add --allow-extra-chr to GenotypeG1G2RiskAlleles by (#96)
• Separate training on population from application of ancestry adjustment in prs pipeline (#91)
• Pass through lab_batch in PRSWrapper, and dynamically find tables (#98)
• PRS missing sites QC (#99)
• Remove personal dockers in PRS pipeline (#100)
• Pass through is_control_sample (#101)
• Aggregate PRS: Added logic to compare control sample vs expected control results by (#102)
• Formatting improvements to aggregation report (#105)

FindSamplesAndBenchmark

• Fixing some issues and updating FindSamplesAndBenchmark (#86)

BenchmarkVCFs

• BenchmarkVCFs: Fixed a bug where NA is written to output files (#89)

General

• Fix copyright in license (#104)