What's Changed
- Bump version after release 3.22.2 by @pinin4fjords in #1663
- Update preprocessing with multiple rRNA removal tools by @pinin4fjords in #1664
- Add ARM containers, changelog updates, and bulk module/subworkflow updates by @pinin4fjords in #1665
- New module for contamination screening: Sylph by @egreenberg7 in #1616
- Enable SeqKit stats MultiQC module for RiboDetector rRNA removal by @pinin4fjords in #1669
- fix: Enhance RSEM output exports and remove unnecessary star_rsem check by @EladH1 in #1667
- Document star_rsem STAR aligner settings and customization by @cmatKhan in #1672
- Apply Nextflow 25 strict syntax fixes by @pinin4fjords in #1677
- fix(tests): Comprehensive PREPARE_GENOME test fixes for proper aligner coverage by @pinin4fjords in #1687
- feat: Migrate to topic-based version reporting by @pinin4fjords in #1689
- feat: Add prokaryotic RNA-seq support with -profile prokaryotic by @pinin4fjords in #1688
- feat: Add support for uncompressed FASTQ input files by @pinin4fjords in #1686
- Fix offline mode by skipping igenomes_base validation by @pinin4fjords in #1696
- refactor: Replace local iGenomes STAR modules with nf-core aliases by @pinin4fjords in #1694
- Add GPU accelerated STAR and Markdups (using Parabricks rna_fq2bam) by @gburnett-nvidia in #1685
- Add FastQC step after BBSplit/rRNA filtering by @pinin4fjords in #1700
- fix: Include single-library samples in merged fastq output by @pinin4fjords in #1704
- feat: Add tximport processing for RSEM outputs (#1320) by @pinin4fjords in #1697
- feat: Enable UMI deduplication with STAR/RSEM aligner by @pinin4fjords in #1707
- fix: Allow pre-built pseudo-aligner index without --fasta by @pinin4fjords in #1708
- docs: update metro map renders with nf-metro v0.4.7 by @pinin4fjords in #1709
- Fix GPU profile applying container flags globally by @pinin4fjords in #1711
- refactor: seq_platform/seq_center via ext.args closures by @pinin4fjords in #1713
- Bump version to 3.23.0 ahead of release by @pinin4fjords in #1715
- Fix: informative error when Salmon strandedness inference fails by @pinin4fjords in #1716
- Add --seq_platform parameter for global sequencing platform RG tag by @pinin4fjords in #1718
- Docs and changelog cleanup by @pinin4fjords in #1719
- Update umitools modules: remove patches, add channel prefixes by @pinin4fjords in #1724
- Refine .nftignore patterns and update test snapshots by @pinin4fjords in #1725
- docs: regenerate metro map with nf-metro v0.5.1 by @pinin4fjords in #1714
- docs: re-render metro map with nf-metro v0.5.4 by @pinin4fjords in #1728
- ci: bump Nextflow to 25.04.3 to fix conda --mkdir bug by @pinin4fjords in #1730
- refactor: code quality improvements from PR #1717 review by @pinin4fjords in #1735
- refactor: compose test_prokaryotic profile on prokaryotic by @pinin4fjords in #1734
- test: load prokaryotic config in nf-test instead of duplicating params by @pinin4fjords in #1736
- Fix iGenomes STAR conda channel for x86_64 by @pinin4fjords in #1738
- Dev -> master for nf-core/rnaseq 3.23.0 by @pinin4fjords in #1717
New Contributors
- @cmatKhan made their first contribution in #1672
- @gburnett-nvidia made their first contribution in #1685
Full Changelog: 3.22.2...3.23.0