3.10.0 - Aktse Added Addition of: Parabricks HaplotypeCaller with --tools parabricks_haplotypecaller by @gburnett-nvidia. This currently produces per-sample VCFs and does not support joint germline calling. Varlociraptor FDR filtering for germline, somatic and tumor-only workflows by @famosab. Bug fixes Fix --normalize_vcfs dropping an allele from multiallelic sites by @apolitics. Fix VEP LoFTEE plugin execution with Conda. Skip nf-schema path validation for --annotation_cache and --igenomes_base by @pinin4fjords. Improvements Prepare the pipeline for Nextflow strict syntax and Nextflow 26. Migrate modules to topic channels. Update Ensembl VEP to 116.0 by @maxulysse. Update bcftools to 1.23.1 by @famosab. Update Parabricks to 4.7.1, GATK to 4.6.2, samtools to 1.24, mosdepth to 0.3.14 and several other dependencies. Update the pipeline template to nf-core/tools 4.1.0. Important changes Somatic FreeBayes no longer uses --pooled-discrete, and its default minimum alternative allele fraction changes from 0.03 to 0.01. When starting from CRAM or BAM files with --step variant_calling, CNVKit output names are now based on the input filename instead of the sample name. FASTQ-based workflows are unaffected. The output format of GATK4_APPLYBQSR and GATK4SPARK_APPLYBQSR can no longer be changed using ext.suffix. New parameters --varlociraptor_events_germline --varlociraptor_events_somatic --varlociraptor_events_tumor_only --varlociraptor_fdr New Contributors @gburnett-nvidia made their first contribution in #2176 @apolitics made their first contribution in #2216 Full Changelog: https://github.com/nf-core/sarek/compare/3.9.0...3.10.0