sarek nf-core/sarek 3.11.0 – Guhkesvákkjåhkå is released! sarek cat jam https://github.com/nf-core/sarek/releases/tag/3.11.0 New: • 🚀 Parabricks DeepVariant (--tools parabricks_deepvariant) for GPU-accelerated germline calling •🚀 Parabricks ApplyBQSR, and Parabricks HaplotypeCaller in gVCF mode for joint calling • 🧬 DeepSomatic and Parabricks DeepSomatic for tumour-normal short-read calling (--tools deepsomatic, --tools parabricks_deepsomatic) • 🔨 New --ascat_penalty parameter (default 70) Changed: • 🪶 GATK 4.6.2.0 → 4.7.0.0 (Lite containers). Recalibrated CRAMs stay CRAM 3.0 so legacy tools can still read them, and CRAI indexes are now published with them. • ⚡ Recalibration now uses the nf-core bam_applybqsr subworkflow • ➕ ensembl-vep 116.3, varlociraptor 8.12.0 • 📖 ASCAT resource docs now point to Zenodo, with clearer WES and targeted-sequencing steps Fixed: • 🐛 Several Parabricks fixes: fq2bam no longer silently produces nothing with --no_intervals or without known sites, BQSR no longer stalls or runs out of memory from unindexed known-sites VCFs, and the germline callers now fail early on tumour-only samplesheets • 🦗 Varlociraptor custom scenario parsing • 🐞 the Spark MarkDuplicates pixel distance • 🐝 BCFtools mpileup prefix Huge thanks to everyone who contributed to this release 🙏 @Gary Burnett, @Rike Hanssen, @Famke Bäuerle, @jfischba, @Adam Talbot, @Edmund, @dlt481, @Phil Ewels, @p, @mashehu, @Peter Z, @Charles-Alexandre Roy, @Agrima Bhattand @Michael Heuer, plus everyone who reported issues and reviewed PRs.