nf-core · kubranarci · Apr 22, 2026 · Dec 3, 2025 · Dec 3, 2025 · Dec 4, 2025
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -13,4 +13,4 @@ template:
   name: variantbenchmarking
   org: nf-core
   outdir: .
-  version: 1.4.0
+  version: 1.5.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,55 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 1.5.0dev
+
+### `Added`
+
+- RTGtools update to 3.13 [#261](https://github.com/nf-core/variantbenchmarking/issues/261)
+- Transforming local modules with bcftools and tabix to standard nf-core modules [#267](https://github.com/nf-core/variantbenchmarking/pull/267)
+- Replace local modules SORT_BED and REFORMAT_HEADER with nf-core ones. [#268](https://github.com/nf-core/variantbenchmarking/pull/268)
+- Replace local module FIX_VCF_PREFIX with BCFTOOLS_ANNOTATE [#287](https://github.com/nf-core/variantbenchmarking/pull/287)
+- Replacing create_datavzrd_input with cat_cat [#292](https://github.com/nf-core/variantbenchmarking/pull/292)
+- 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](https://github.com/nf-core/variantbenchmarking/pull/276)
+- Syntax health, Channel to channel, versions to topic channels. Version update for happy, bedops, picard, ucsc, datavzrd, truvari tools [#277](https://github.com/nf-core/variantbenchmarking/pull/277)
+- Bedfile index checking and smoother vcf comparisions [#290](https://github.com/nf-core/variantbenchmarking/pull/290)
+- Adding nf-tests to local modules [#278](https://github.com/nf-core/variantbenchmarking/pull/295/), thanks @aaryanjaitly for initiation of some processes.
+- Replace local module VARIANT_EXTRACTOR with nf-core module VARIANTEXTRACTOR [#278](https://github.com/nf-core/variantbenchmarking/pull/295/)
+- Adding nf-test and meta.yml to local subworklfows, removing overlapping workflow tests [#257](https://github.com/nf-core/variantbenchmarking/pull/296)
+- Adding rtgtools cnveval as a new benchmarking method for copynumber variants [#298](https://github.com/nf-core/variantbenchmarking/pull/298).
+
+### `Fixed`
+
+- increasing font sizes, making labelling optional and some fixes around plots. Tests are editted to observe optional plot arguments. [#270](https://github.com/nf-core/variantbenchmarking/pull/270)
+- Improving the pipeline towards strict syntax health & adding topic channels - 1 [#272](https://github.com/nf-core/variantbenchmarking/pull/272)
+- Syntax health, Channel to channel, versions to topic channels. Version update for happy, bedops, picard, ucsc, datavzrd, truvari tools [#277](https://github.com/nf-core/variantbenchmarking/pull/277)
+- Fixing the bed file bug in concordance analysis [#260](https://github.com/nf-core/variantbenchmarking/pull/275)
+- Missing --sample for meta.id is fixed in BCFTOOLS_REHEADER [#276](https://github.com/nf-core/variantbenchmarking/pull/276)
+- GT field is necessary for rtgtools vcfeval, strelka reports no GT field for somatic analysis. Fixing the GT field setup for strelka (bcftools plugingtset doesnt work as GT is not available) [#279](https://github.com/nf-core/variantbenchmarking/pull/279)
+- Using nf-metro to create better metromap [#281](https://github.com/nf-core/variantbenchmarking/pull/281)
+- Remove unneccesery reheadering of the vcf outputs of rtgtools and truvari [#286](https://github.com/nf-core/variantbenchmarking/pull/286)
+- Fixing bugs: bnd vcfeval output files producing tags with [] and reformatting header before merging in ensemble analysis [#297](https://github.com/nf-core/variantbenchmarking/pull/297)
+- sv_germline_benchmarking subworkflow renamed to sv_benchmarking as we use the same subworkflow for both germline and somatic analysis [#298](https://github.com/nf-core/variantbenchmarking/pull/298).
+- Preparing for the release 1.5.0 and fixing linting errors [#299](https://github.com/nf-core/variantbenchmarking/pull/299).
+- Applying review comments before 1.5.0 release [#231](https://github.com/nf-core/variantbenchmarking/pull/301)
+
+### `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         |
+
 ## 1.4.0
 
 ### `Added`

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -18,6 +18,8 @@
 
 ## [nf-co2footprint](https://github.com/nextflow-io/nf-co2footprint)
 
+## [nf-metro](https://github.com/pinin4fjords/nf-metro)
+
 ## Pipeline tools
 
 - [Bcftools](http://samtools.github.io/bcftools/bcftools.html)

diff --git a/README.md b/README.md
@@ -27,28 +27,47 @@
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
-<p align="center">
-    <img title="variantbenchmarking metro map" src="docs/images/variantbenchmarking_metromap.png" width=100%>
-</p>
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/variantbenchmarking.svg">
+  <img alt="nf-core/variantbenchmarking metro map" src="docs/images/variantbenchmarking.svg">
+</picture>
 
 The workflow involves several key processes to ensure reliable and reproducible results as follows:
 
-### Standardization and normalization of variants:
+### Standardization and normalization of test (query/comparison) variants:
 
 This initial step ensures consistent formatting and alignment of variants in test and truth VCF files for accurate comparison.
 
-- Subsample if input test vcf is multisample ([bcftools view](https://samtools.github.io/bcftools/bcftools.html#view))
-- Homogenization of multi-allelic variants, MNPs and SVs (including imprecise paired breakends and single breakends) ([variant-extractor](https://github.com/EUCANCan/variant-extractor))
-- Reformatting test VCF files from different SV callers ([svync](https://github.com/nvnieuwk/svync))
+- Subsample if input vcf is multisample ([bcftools view](https://samtools.github.io/bcftools/bcftools.html#view))
+- Homogenization of multi-allelic variants, MNPs and SVs to BND (including imprecise paired breakends and single breakends) ([variant-extractor](https://github.com/EUCANCan/variant-extractor))
+- Reformatting VCF files from different SV callers ([svync](https://github.com/nvnieuwk/svync))
 - Standardize SV variants to BND ([SVTK standardize](https://github.com/broadinstitute/gatk-sv/blob/main/src/svtk/scripts/svtk))
 - Decompose SVs to BND [rtgtools svdecompose](https://cn.animalgenome.org/bioinfo/resources/manuals/RTGOperationsManual.pdf)
-- Rename sample names in test and truth VCF files ([bcftools reheader](https://samtools.github.io/bcftools/bcftools.html#reheader))
-- Splitting multi-allelic variants in test and truth VCF files ([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
-- Deduplication of variants in test and truth VCF files ([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
-- Left aligning of variants in test and truth VCF files ([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
-- Use prepy in order to normalize test files. This option is only applicable for happy benchmarking of germline analysis ([prepy](https://github.com/Illumina/hap.py/tree/master))
+- Rename sample names ([bcftools reheader](https://samtools.github.io/bcftools/bcftools.html#reheader))
+- Splitting multi-allelic variants([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
+- Deduplication of variants ([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
+- Left aligning of variants ([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
+- Use prepy in order to normalize. This option is only applicable for happy benchmarking of germline analysis ([prepy](https://github.com/Illumina/hap.py/tree/master))
 - Split SNVs and indels if the given test VCF contains both. This is only applicable for somatic analysis ([bcftools view](https://samtools.github.io/bcftools/bcftools.html#view))
 
+### Standardization and normalization of truth (baseline) variants:
+
+- Decompose SVs to BND [rtgtools svdecompose](https://cn.animalgenome.org/bioinfo/resources/manuals/RTGOperationsManual.pdf)
+- Rename sample names ([bcftools reheader](https://samtools.github.io/bcftools/bcftools.html#reheader))
+- Splitting multi-allelic variants ([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
+- Deduplication of variants ([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
+- Left aligning of variants([bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm))
+
+### Ensemble (majority rule) approch to prepare truth variants:
+
+When a "Gold Standard" (a high-confidence, validated set of variants) is not available, you can create a Proxy Ground Truth by looking for agreement between different tools. This is Majority Rule approach assumes that if multiple independent variant callers identify the same mutation, it is more likely to be a real biological variant rather than a technical error from a single pipeline. Only variants found by at least the minimum number of callers specified in your threshold are kept as the "truth" for the final benchmark.
+
+If the $--ensemble/_truth$ threshold is set higher than 0, the pipeline performs the following steps:
+
+- Merge small (SNVs and INDELs) using ([bcftools merge](https://samtools.github.io/bcftools/bcftools.html#merge))
+- Merge Structual Variants using ([SURVIVOR merge](https://github.com/fritzsedlazeck/SURVIVOR/wiki))
+- Consensus filtering the variants according to $--ensemble/_truth$.
+
 ### Filtering options:
 
 Applying filtering on the process of benchmarking itself might makes it impossible to compare different benchmarking strategies. Therefore, for whom like to compare benchmarking methods this subworkflow aims to provide filtering options for variants.
@@ -80,7 +99,7 @@ Available methods for germline and somatic _structural variant (SV)_ benchmarkin
 
 - Truvari ([truvari bench](https://github.com/acenglish/truvari/wiki/bench))
 - SVanalyzer ([svanalyzer benchmark](https://github.com/nhansen/SVanalyzer/blob/master/docs/svbenchmark.rst))
-- Rtgtools (only for BND) ([rtg bndeval](https://realtimegenomics.com/products/rtg-tools))
+- RTGtools (only for BND) ([rtg bndeval](https://realtimegenomics.com/products/rtg-tools))
 
 > [!NOTE]
 > Please note that there is no somatic specific tool for SV benchmarking in this pipeline.
@@ -89,6 +108,7 @@ Available methods for germline and somatic _CNVs (copy number variations)_ are:
 
 - Truvari ([truvari bench](https://github.com/acenglish/truvari/wiki/bench))
 - Wittyer ([witty.er](https://github.com/Illumina/witty.er/tree/master))
+- RTG tools ([rtg cnveval](https://realtimegenomics.com/products/rtg-tools))
 - Intersection ([bedtools intersect](https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html))
 
 > [!NOTE]
@@ -201,6 +221,7 @@ We thank the following people for their extensive assistance in the development
 
 - Nicolas Vannieuwkerke ([@nvnienwk](https://github.com/nvnieuwk))
 - Maxime Garcia ([@maxulysse](https://github.com/maxulysse))
+- Georgia Kesisoglou ([@georgiakes](https://github.com/georgiakes))
 - Sameesh Kher ([@khersameesh24](https://github.com/khersameesh24))
 - Florian Heyl ([@heylf](https://github.com/heyl))
 - Krešimir Beštak ([@kbestak](https://github.com/kbestak))

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/variantbenchmarking/releases/tag/1.4.0" target="_blank">nf-core/variantbenchmarking</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/variantbenchmarking/1.4.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/variantbenchmarking/releases/tag/1.5.0" target="_blank">nf-core/variantbenchmarking</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/variantbenchmarking/1.5.0/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-variantbenchmarking-methods-description":

diff --git a/bin/fix_vcf_prefix.py b/bin/fix_vcf_prefix.py