1.5.0 Vegetarian Han

What's Changed

• Replace local modules: SORT_BED, REFORMAT_HEADER, VARIANT_EXTRACTOR, bcftools, tabix, fix_vcf_prefix, create_datavzrd_input @georgiakes and @kubranarci #267, #268 #292 #287
• Strict syntax health, versions to topics channels - by @kubranarci in #272 #277
• Introducing a new subworkflow to generate truth vcf with an ensemble approach. Test VCFs are being merged and according to ensembl_truth rule (the minimum number of callers to agree) a new truth set is created. This apporach is especially important and needed for somatic benchmarks where truth is often missing. #276
• Updating metromap by @kubranarci in #281
• Issue # 256 bed sanity checking by @Qwertille42 in #290
• Remove unnecessary reheader module form benchmarking by @georgiakes in #286
• Adding tests to local modules by @kubranarci in #295
• Adding tests and meta.yml subworkflows by @kubranarci in #296
• Fixing bugs in bndeval outputs and ensemble analysis by @kubranarci in #297
• Fixing strelka processing by @kubranarci in #279
• Adding rtg cnveval as benchmark method for copynumber variants by @kubranarci in #298

New Dependencies

Dependency	Old version	New version
rtgtools	3.12.1	3.13
bcftools	1.2	1.22
tabix	1.19.1	1.21
bcftools/stats	1.18	1.22
happy	0.3.14	0.3.15
bedops	2.4.41	2.4.42
picard	3.2.0	3.4.0
ucsc	377	482
datavzrd	2.36.12	2.63.3
truvari	5.3.0	5.4.0
gawk	-	5.3.0
coreutils	-	9.5

New Contributors

• @Qwertille42 made their first contribution in #290

Full Changelog: 1.4.0...1.5.0

1.4.0 Thin Yasar

What's Changed

• Pipeline Release 1.4.0 by @kubranarci in #253

New functions

• Adding concordance analysis for query samples by @kubranarci in #237
• 239 add happy sompy and truvari in multiqc report by @kubranarci in #249
• reformat of plot_svlen by @VictorDidier in #250
• add nf-co2footprint by @kubranarci in #228
• 162 use svtk standardize to standardize svs by @kubranarci in #218
• Add hirse promo badge by @kubranarci in #217

Tool updates

• Update multiqc by @georgiakes in #241
• update svync by @kubranarci in #219
• 212 update truvari tools to latest by @kubranarci in #215

Template updates

• nf-core/tools v3.4.1 by @nf-core-bot in #235
• nf-core/tools v3.5.1 by @nf-core-bot in #252

Fixes

• solve bug caused with nf-schema by @kubranarci in #234
• Fix-multisample-processing by @kubranarci in #251
• 229 fn altref is missing in summarycomparisons by @kubranarci in #230
• Change conda channel for matplotlib by @georgiakes in #243
• 220 standardize headers by @kubranarci in #221
• stabilize test files in sarek by @kubranarci in #214

New Contributors

• @georgiakes made their first contribution in #241
• @VictorDidier made their first contribution in #250

Full Changelog: 1.3.0...1.4.0

1.3.0 Solitary Marquez

What's Changed

• adding a tests profile to show ga4gh running params by @kubranarci in #189
• Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in #193
• intersection cannot handle both vcf and bed inputs by @kubranarci in #192
• sompy features table can be used for metrics comparisons by @kubranarci in #194
• Add rtgtools bndeval for BND type benchmarking by @kubranarci in #195
• supply happy comparisons table by @kubranarci in #197
• Add precision vs recall plots by @AtaJadidAhari in #198
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in #200
• Make-tests-more-realistic by @kubranarci in #204
• Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in #205
• prepare-release-1-3-0 by @kubranarci in #207
• change container in pybedtools by @kubranarci in #210
• Pipeline release 1.3.0 by @kubranarci in #206

New Contributors

• @AtaJadidAhari made their first contribution in #198

Full Changelog: 1.2.0...1.3.0

1.2.0 Doubtful Adams

What's Changed

• 159 custom bed files by @kubranarci in #167
• Json schema improvements by @nvnieuwk in #168
• logo cleanup by @kbestak in #171
• modify bcftools_reheader to local by @kubranarci in #170
• Prepare minor version 1.2.0 by @kubranarci in #172
• add changelog by @kubranarci in #175
• Apply reviewer commands 1 2 0 by @kubranarci in #176
• Minor release 1.2.0 by @kubranarci in #173

New Contributors

• @kbestak made their first contribution in #171

Full Changelog: 1.1.0...1.2.0

1.1.0 Dark Murakami

What's Changed

• typo in README.md by @Jessime in #157
• add zenado id by @kubranarci in #158
• implement rtgtools for somatic small bench by @kubranarci in #160
• 161 cnv benchmark subworkflow by @kubranarci in #163
• apply luisas review by @kubranarci in #165
• fix download_pipeline.yml by @kubranarci in #166
• Minor release: 1.1.0 with CNV benchmark subworkflow by @kubranarci in #164

New Contributors

• @Jessime made their first contribution in #157

Full Changelog: 1.0.0...1.1.0

1.0.0 Innocent Pamuk

First release! by @kubranarci

What's Changed

• pin nf-validation version by @nvnieuwk in #6
• wittyer added by @kubranarci in #24
• sv + small analysis implemented by @kubranarci in #30
• sv benchmark params are exposed by @kubranarci in #34
• Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in #37
• 35 add a script to merge benchmarking results by @kubranarci in #40
• 41 somatic benchmarking by @kubranarci in #43
• 16 add survivor merge by @kubranarci in #47
• wittyer fixed by @kubranarci in #51
• plot script fixed by @kubranarci in #53
• rtgtools fix by @kubranarci in #56
• 58 test variant extractor for svs by @kubranarci in #60
• svync input channel is fixed by @kubranarci in #61
• 57 fix prepy + rtgtools eval comb by @kubranarci in #63
• 46 add sv benchmarking for somatic by @kubranarci in #70
• Updating the JSON schemas by @nvnieuwk in #73
• 71 add support for multi sample files by @kubranarci in #75
• 44 add aws full test by @kubranarci in #76
• 77 add liftover option for truths by @kubranarci in #78
• metromap file updated updated by @kubranarci in #87
• 52 use datavzrd to create reports that are usable with ncbench by @kubranarci in #99
• 113 enable liftover option for test vcfs by @kubranarci in #115
• Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in #137
• adding full size aws tests by @kubranarci in #142
• 95 release v100 requirements by @kubranarci in #147
• changes requested by Nicolas by @kubranarci in #151
• Release pipeline v1.0.0 by @kubranarci in #148

New Contributors

• @maxulysse made their first contribution in #2
• @nvnieuwk made their first contribution in #6
• @nf-core-bot made their first contribution in #3

Full Changelog: https://github.com/nf-core/variantbenchmarking/commits/v1.0.0