🦭 nf-core/rnaseq 3.24.0 (Selenium Seahorse) is out! A focused but impactful release - highlights: ⚡ RustQC: optional single-pass QC A new

--use_rustqc

option adds @Phil Ewels' RustQC as a fast, single-pass replacement for the post-alignment QC steps (RSeQC, Preseq, Qualimap, Dupradar + more). It's an exciting new tool and we'd love to hear how people find it in practice! 🔀 Per-sample tximport with

--skip_quantification_merge

A new flag that runs tximport independently per sample rather than merging, giving more flexibility for downstream analysis workflows. 🦠 Kraken2 contamination screening pre-alignment New --contaminant_screening_input parameter lets you run contamination screening (Kraken2, Bracken, or Sylph) on trimmed reads before alignment, rather than only on aligner-unmapped reads. Thanks @Elad Herz! 🔧 Other notable changes: • Always set ID/SM BAM read group tags (fixing an inconsistency from 3.23.0) •

igenomes_base

validation now always skipped in offline mode • Bowtie2 module fixed for version extraction with Perl locale warnings • iGenomes STAR version detection and index building logic corrected • STAR removed from RSEM conda environments for ARM64 compatibility •

extra_star_align_args

deduplication restored to prevent duplicate parameter errors • Bowtie2 rRNA removal now correctly distinguished from alignment in MultiQC • samtools updated to 1.23.1, RiboDetector to 0.3.3, RustQC to 0.2.1 • nf-core template bumped to v3.5.2 • 📖 Docs: GFF files must be passed via

--gff

, and test profile requirement for local nf-test runs clarified 🙏 Thanks to everyone who contributed to this release, including everyone who reported bugs/ made feature requests/ reviewed PRs. 📋 Full changelog and release: https://github.com/nf-core/rnaseq/releases/tag/3.24.0 🐛 Bugs and feature requests to https://github.com/nf-core/rnaseq/issues!