nf-core/rnaseq: nf-core/rnaseq v3.23.0 - Gallium Gecko

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