What’s Changed

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

New Contributors

• @AtaJadidAhari made their first contribution in https://github.com/nf-core/variantbenchmarking/pull/198

Full Changelog: https://github.com/nf-core/variantbenchmarking/compare/1.2.0…1.3.0

What’s Changed

• 159 custom bed files by @kubranarci in https://github.com/nf-core/variantbenchmarking/pull/167
• Json schema improvements by @nvnieuwk in https://github.com/nf-core/variantbenchmarking/pull/168
• logo cleanup by @kbestak in https://github.com/nf-core/variantbenchmarking/pull/171
• modify bcftools_reheader to local by @kubranarci in https://github.com/nf-core/variantbenchmarking/pull/170
• Prepare minor version 1.2.0 by @kubranarci in https://github.com/nf-core/variantbenchmarking/pull/172
• add changelog by @kubranarci in https://github.com/nf-core/variantbenchmarking/pull/175
• Apply reviewer commands 1 2 0 by @kubranarci in https://github.com/nf-core/variantbenchmarking/pull/176
• Minor release 1.2.0 by @kubranarci in https://github.com/nf-core/variantbenchmarking/pull/173

New Contributors

• @kbestak made their first contribution in https://github.com/nf-core/variantbenchmarking/pull/171

Full Changelog: https://github.com/nf-core/variantbenchmarking/compare/1.1.0…1.2.0

What’s Changed

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

New Contributors

• @Jessime made their first contribution in https://github.com/nf-core/variantbenchmarking/pull/157

Full Changelog: https://github.com/nf-core/variantbenchmarking/compare/1.0.0…1.1.0

First release! by @kubranarci

What’s Changed

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

New Contributors

• @maxulysse made their first contribution in https://github.com/nf-core/variantbenchmarking/pull/2
• @nvnieuwk made their first contribution in https://github.com/nf-core/variantbenchmarking/pull/6
• @nf-core-bot made their first contribution in https://github.com/nf-core/variantbenchmarking/pull/3

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