What's Changed
- fix: always set ID/SM read group tags; bump version to 3.24.0dev by @pinin4fjords in #1740
- fix: always skip igenomes_base validation by @pinin4fjords in #1745
- fix: update bowtie2 modules to fix version extraction with Perl locale warnings by @pinin4fjords in #1749
- docs: add missing tool citations to CITATIONS.md by @pinin4fjords in #1750
- feat: add --skip_quantification_merge for per-sample tximport by @pinin4fjords in #1744
- docs: clarify GFF files must use --gff parameter by @pinin4fjords in #1751
- Add evaluation of trimmed data and aligners kranken - check contamination before aligners - enhancement by @EladH1 in #1746
- Fix iGenomes STAR version detection and index building logic by @pinin4fjords in #1756
- fix: remove STAR from RSEM conda environments for ARM compatibility by @pinin4fjords in #1752
- fix: restore extra_star_align_args dedup to prevent STAR duplicate parameter error by @pinin4fjords in #1762
- fix: distinguish Bowtie2 alignment from rRNA removal in MultiQC report by @pinin4fjords in #1761
- Add RustQC as optional single-pass QC replacement by @pinin4fjords in #1754
- chore: Update nf-core template to v3.5.2 by @pinin4fjords in #1764
- Bump version to 3.24.0 ahead of release by @pinin4fjords in #1763
- Update samtools modules to 1.23.1 by @pinin4fjords in #1766
- Remove --star from RSEM preparereference test config by @pinin4fjords in #1769
- Exclude non-deterministic qualimap multiqc files from snapshots by @pinin4fjords in #1770
- Update actions/upload-artifact from v3 to v7 in cloud test workflows by @pinin4fjords in #1768
- Update ribodetector module to 0.3.3 by @pinin4fjords in #1771
- Update ribodetector ARM64 container to 0.3.3 by @pinin4fjords in #1772
- Fix megatest debug log upload on launch failure by @pinin4fjords in #1774
- Update RustQC to 0.2.1 by @pinin4fjords in #1779
- docs: clarify test profile requirement for local nf-test runs by @pinin4fjords in #1778
- Dev -> master for nf-core/rnaseq 3.24.0 by @pinin4fjords in #1765
Full Changelog: 3.23.0...3.24.0