🦅 nf-core/rnaseq 3.27.0 (Vanadium Vulture) is out! Bigger release this time - new pipeline options, a stack of edge-case fixes, and two template updates. Highlights: 🧬 New contaminant screening + rRNA index options •

--contaminant_screening_input trim_only|raw

lets you screen for contaminants right after adapter trimming (before BBSplit/rRNA removal) or on raw reads as a baseline, catching species a narrow BBSplit index would otherwise silently drop (thanks @Elad Herz) •

--bowtie2_rrna_index

accepts a pre-built Bowtie2 index for rRNA removal, skipping on-the-fly index construction from

--ribo_database_manifest

📦 STAR index fix for object-storage work directories •

STAR_GENOMEPARAMS_UPGRADE

(the same step that got legacy iGenomes indices running on ARM last release) was symlinking index files instead of copying them. Fine on a local/NFS work dir, but it breaks on object-storage-backed ones like Azure Batch via azcopy, which can't represent symlinks - indices could come out broken or missing. Now copies instead 🚀 GPU STAR (Parabricks) bumped to 4.7.1 • Thanks @Gary Burnett (NVIDIA) for keeping the Parabricks rna_fq2bam integration current 📊 Fixes for crashes and quiet correctness bugs: • StringTie merge now completes with warnings instead of crashing when every sample fails

--min_mapped_reads

, and its `--fr`/`--rf` strandedness flags are back after being dropped with no replacement in that same module update • Salmon auto-strandedness inference no longer crashes on kallisto-only runs with no

--fasta

• Biotype QC now warns instead of crashing when a GTF has no per-transcript biotype attribute, e.g. NCBI annotations •

--use_rustqc

works with UMI-deduplicated BAMs instead of aborting on the duplicate-marking check — UMI dedup removes PCR duplicates outright, so there's nothing left to flag (thanks @Felix Krueger) • TrimGalore gets a real 4 GB memory allocation instead of the 1 GB

process_low_memory

default that was OOM-killing every sample on every retry (thanks @Felix Krueger) • MultiQC's mapping-rate warning now names the aligner actually in use instead of always saying "STAR" 🔧 Other notable changes: • Nextflow floor raised to 25.10.4,

nf-schema

bumped to 2.7.2 • Sync nf-core template to v4.0.3 and v4.1.0 • New

--extra_hisat2_align_args

and

--extra_salmon_index_args

passthrough options (thanks @Maxime Garcia) •

manifest.diagram

now points at the metro map (thanks @Phil Ewels) • Module bumps:

trimgalore

2.3.0,

tximeta/tximport

,

quantify_rsem

, StringTie, HISAT2 and more 🙏 Thanks to everyone who contributed - bug reports, feature requests, reviews and code all very appreciated. 📋 Full changelog and release: github.com/nf-core/rnaseq/…/3.27.0 🐛 Bugs and feature requests to github.com/nf-core/rnaseq/issues!