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