A big release with new user-facing options, several bug fixes for edge cases (Azure, NCBI GTFs, kallisto-only runs, UMI-deduplicated BAMs), and two nf-core template updates.
New features
- Screen contaminants pre-trimming or post-trimming, not just post-BBSplit/rRNA-removal, via
--contaminant_screening_input trim_only|raw(#1878 by @EladH1) - Supply a pre-built Bowtie2 index for rRNA removal with
--bowtie2_rrna_index, skipping on-the-fly index construction (#1892 by @emmanuel-tan) - New passthrough args:
--extra_hisat2_align_args(#1913 by @maxulysse),--extra_salmon_index_args(#1923) manifest.diagramnow points at the metro map (#1915 by @ewels)
Fixes
- Copy instead of symlink STAR index files, fixing broken indices on object-storage work directories like Azure Batch (#1911)
- Restore StringTie's
--fr/--rfstrandedness flags, dropped by a module update with no replacement (#1924) - Let StringTie merge complete with warnings instead of crashing when every sample fails
--min_mapped_reads(#1902) - Fix Salmon auto-strandedness crash on kallisto-only (no
--fasta) runs (#1907) - Skip biotype QC with a warning instead of crashing when a GTF lacks per-transcript biotype attributes, e.g. NCBI annotations (#1919)
--use_rustqcnow works with UMI-deduplicated BAMs instead of aborting on the duplicate-marking check (#1882 by @FelixKrueger)- Give TRIMGALORE a real 4 GB memory allocation, fixing an OOM that hit every sample on every retry (#1905 by @FelixKrueger)
- MultiQC now shows the active aligner's name in mapping-rate warnings instead of hardcoding "STAR" (#1850)
Updates
- Raise the minimum Nextflow version to 25.10.4 and bump
nf-schemato 2.7.2 (#1680, #1864) - Template updates for nf-core/tools v4.0.3 and v4.1.0 (#1894, #1914)
- Module bumps:
trimgalore2.3.0,tximeta/tximport,quantify_rsem, StringTie, HISAT2, and GPU STAR (Parabricks) to 4.7.1 (#1899 by @gburnett-nvidia)
See the full changelog for all 40 merged PRs.
Credits
Special thanks to the following for their contributions to the release:
- Adam Talbot
- apeleraux
- Daniel Lundin
- Davide Bressan
- dawnmy
- Dmytro Hlushchenko
- EladH1
- emmanuel-tan
- Evangelos Karatzas
- Felix Krueger
- Friederike Hanssen
- Gary Burnett
- Ido Tamir
- Jose Espinosa-Carrasco
- Joseph Longworth
- Luisa Santus
- Mahesh Binzer-Panchal
- Matthias Hörtenhuber
- Matthias Zepper
- Maxime U Garcia
- murphyte
- mvheetve
- Paolo Inglese
- Phil Ewels
Full Changelog: 3.26.0...3.27.0