1.6.0 Nominal Eco

What's Changed

nf-core/variantbenchmarking 1.6.0 – Nominal Eco

Highlights

• New benchmarking method: Aardvark for small variants (--method aardvark). Results are merged into the summary tables with TP/FP/FN, precision, recall, F1 and genotype-level FN/FP counts (#315)
• Interactive reports: all summary plots (metrics, upset, length distributions) are now interactive HTML instead of static PNG (#325)
• New hap.py stratified HTML report, generated from stratified hap.py results (#326)
• New --skip_reports parameter: comma-separated list (datavzrd, happy) to turn off optional report generation (#356)
• Concordance analysis can be limited to specific truth/query pairs, so you no longer have to run every pairwise comparison (#348)
• Visualising results in Depictio (#345)

Changed

• hap.py now runs in a container that also includes rtgtools (#327); the Singularity image is gzip-enabled (#334)
• Local VCF_VARIANT_FILTERING replaced by the nf-core subworkflow VCF_FILTER_SURVIVOR_BCFTOOLS (#349)
• Local tabix module replaced by the nf-core htslib/bgziptabix module (#329)
• BED files for small-variant analysis reorganised (#319)
• Pipeline template updated to nf-core/tools v4.2.1, via v4.0.0, v4.0.2, v4.0.3 and v4.1.0 (#304, #305, #317, #322, #355)

Fixed

• Liftover: target_bed was not passed through and is now included (#320)
• Sample-ID conflicts when the same sample name occurs in several inputs (#336)
• Sample IDs in truth files produced by rtgtools are now set correctly (#337)

Performance

• VCF_TO_CSV streams records instead of keeping the whole VCF in memory, which lowers memory use on large VCFs (#331)
• Upset plot generation optimised to avoid out-of-memory failures on large comparisons (#339)

Removed / deprecated

Warning

These changes may require updating existing parameter files or downstream scripts.

• pre.py preprocessing deprecated(#316)
• Small-variant splitting subworkflow removed (#354)
• Plot outputs are now .html instead of .png; adjust any downstream scripts that look for PNG files (#325)
• Concordance runs only the requested pairs rather than all combinations (#348)

CI / infrastructure

• Removed a vulnerable PR-comment artifact pattern (#318)
• fix-linting switched to the hardened nf-core/actions reusable workflow (#333)
• New nf-diff PR check and baseline workflows to catch output changes between versions (#344); Nextflow version pinned and results posted via pr-comment.yml (#346)

Software dependencies

Dependency	Old version	New version
pigz	2.8	deprecated
nf-core	3.5.1	4.1.0
prettier	3.6.2	3.8.3
prepy	0.3.15	deprecated
r-base	4.1.0	deprecated
ga4gh-happy-report	-	0.1.2
rtg-tools (hap.py)	-	3.13
tabix	1.21	deprecated
htslib	-	1.24
xz	-	5.8.3
nf-schema	2.5.1	2.7.3
Nextflow	25.04.0	25.10.4
multiqc	1.32	1.33

• New parameters: skip_plots, skip_reports, high_conf, happy_comparison_engine
• Depreciated parameters: falsepositive_bed

Contributors

Thanks to @kubranarci, @georgiakes, @edogiuili, @mashehu, @adamrtalbot and @nf-core-bot.

New contributors: @mashehu (#318), @adamrtalbot (#331), @edogiuili (#345) – welcome!

Full changelog: 1.5.0...1.6.0