🦑 nf-core/rnaseq 3.26.0 (Chromium Cuttlefish) is out! Tighter release this time — reproducibility, containers, and infrastructure. Highlights: ⚡ TrimGalore 2.1.0 (Oxidized Edition) @Felix Krueger’s Full Rust rewrite of what was a Perl-on-Cutadapt-on-Python stack. Adapter trimming reimplemented in-process, so the per-read cost drops, parallelism scales near-linearly to 8 cores instead of bottlenecking on Cutadapt's threading, and gzip output is written at level 1 by default - substantially faster on multi-core runs. Output is byte-identical to 0.6.x. Container is a single static binary, multi-arch amd64 + arm64. Also eliminates use of intermediate files matching the output patterns, that were starting to generate bug reports for us in some scenarios. 🚀 Drop the parallel STAR 2.6.1d pin (legacy iGenomes indices now run on ARM) Legacy iGenomes STAR indices used to force the pipeline onto a separately containerised STAR 2.6.1d build with no ARM variant - making iGenomes runs effectively x86-only. Genome-map entries flagged

star_legacy = true

now route through a new

STAR_GENOMEPARAMS_UPGRADE

step that rewrites

genomeParameters.txt

to the 2.7.4a schema in-place, so the modern multi-arch STAR build the pipeline already ships handles them. ARM users (Graviton, Apple Silicon) can now run the existing iGenomes catalogue. Sentieon and Parabricks STAR branches bypass the upgrade. Credit @Thomas Danhorn for the idea 📊 MultiQC and reproducibility fixes - Disambiguate the three FastQC instances in MultiQC General Statistics with

(raw)

/

(trim)

/

(filt)

suffixes (#1828) - Publish

*.merged.tx2gene_augmented.tsv

— the table

tximport

actually consumes, required to reproduce gene-level outputs from per-sample quants (#1830) - Suppress non-comparable

*gene_counts_length_scaled.tsv

under

--skip_quantification_merge

(#1822) - Sort merged Strandedness checks tables by sample id for deterministic md5 🔧 Other notable changes: - Sync nf-core template to v4.0.2 - Add

process_low_memory

(1 GB) label to

conf/base.config

for the new TrimGalore upstream label - Rename legacy STAR scaffolding (

use_igenomes_star

,

STAR_ALIGN_IGENOMES

,

conf/igenomes_star.config

) to

legacy

-prefixed equivalents 🙏 Thanks to everyone who contributed - bug reports, feature requests, reviews and code all very appreciated. 📋 Full changelog and release: https://github.com/nf-core/rnaseq/releases/tag/3.26.0 🐛 Bugs and feature requests to https://github.com/nf-core/rnaseq/issues!