What's Changed Bump version to 3.25.0dev; fix SortMeRNA sample name in MultiQC by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1781 refactor: delocalise GTF_FILTER to nf-core custom/gtffilter by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1782 fix: wire up skip_gtf_transcript_filter to CUSTOM_GTFFILTER ext.args by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1783 Replace local gtf2bed with nf-core ea-utils/gtf2bed module by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1784 refactor: replace local BAM QC with nf-core bam_qc_rnaseq subworkflow by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1786 feat: add GPU support for ribodetector by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1790 refactor: centralize module configs in conf/modules/ by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1788 Bump custom/multiqccustombiotype to fail loudly on high biotype cardinality by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1795 feat: add strand-agnostic bigwig, skip per-strand for unstranded libraries by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1792 Fix MultiQC collapsing _1/_2 sample IDs via per-sample lookbehind by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1793 docs: clarify prokaryotic transcript extraction includes tRNA/rRNA/tmRNA/ncRNA by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1796 Add stringtie_merge for de novo assembly by @Odulhin in https://github.com/nf-core/rnaseq/pull/1755 fix(prokaryotic): skip StringTie by default in the prokaryotic profile by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1804 fix: per-sample MultiQC progressive closure via structural .join chain by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1803 feat(bowtie2_salmon): report up to -k 200 alignments so Salmon EM can work by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1806 fix(sortmerna): adopt SortMeRNA SILVA 138 smr_v4.3_default_db as the default rRNA database by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1811 fix(mqc): strandedness table rows reflect which analyses ran; narrow prokaryotic RSeQC skip by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1805 test: dedupe pipeline-level tests without losing coverage by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1812 chore: sync nf-core components and retire ch_versions plumbing by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1814 test(cleanup): gate pipeline-test cleanup on CI to keep local reruns stable by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1815 Bump version to 3.25.0 ahead of release by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1799 fix(prokaryotic): derive gene BED via gffread --bed by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1817 chore: drop redundant versions.yml filters from saveAs closures by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1818 fix(prokaryotic): skip RSeQC infer_experiment on bowtie2_salmon + skip sentieon on conda by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1819 Dev -> master for nf-core/rnaseq 3.25.0 by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1816 New Contributors @Odulhin made their first contribution in https://github.com/nf-core/rnaseq/pull/1755 Full Changelog: https://github.com/nf-core/rnaseq/compare/3.24.0...3.25.0